Thermo Easy NLC Service Manual PDF

Thermo
EASY-nLC Series
Troubleshooting and
Maintenance Guide
(Software version 3.1)
60053-97228 Revision B January 2013

© 2013 Thermo Fisher Scientific Inc. All rights reserved.
EASY-nLC, AFC, IFC, nanoViper, and PepMap are trademarks and Acclaim, Dionex, LCQ Fleet, LXQ, LTQ,
and Xcalibur are registered trademarks of Thermo Fisher Scientific Inc.
PEEK is a trademark of Victrex PLC. PEEKsil is a trademark of SGE International Pty Ltd Corp.
This product uses FreeRTOS from www.freertos.org (available upon request). FreeRTOS is a registered
trademark of Real Time Engineers Ltd.
The following are registered trademarks in the United States: Advion and RePlay are registered trademarks of
Advion BioSystems, Inc. CMOSens is a registered trademark of Sensirion AG Corp. Duran is a registered
trademark of Schott AG. PhotoMOS is a registered trademark of Panasonic Electric Works, Co., Ltd. Teflon is
a registered trademark of E.I. du Pont de Nemours and Company. VICI and Valco are registered trademarks of
Valco Instruments Co., Inc.
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All other trademarks are the property of Thermo Fisher Scientific and its subsidiaries.
Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
product operation. This document is copyright protected and any reproduction of the whole or any part of this
document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.
The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.
Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or error-
free and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might
result from any use of this document, even if the information in the document is followed properly.
This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This
document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of
Sale shall govern all conflicting information between the two documents.
Release history: Revision A, March 2012; Revision B, January 2013. Revision B includes information about
replacing a PLF pump with a PLU pump, information about upgrading the touch-screen software, and
improved troubleshooting procedures.
Hardware versions: EASY-nLC II and EASY-nLC 1000 instruments
Software version: Touch-screen software version 3.1
For Research Use Only. Not for use in diagnostic procedures.
Regulatory Compliance
Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with
applicable domestic and international regulations. When the instrument is delivered to you, it meets all pertinent
electromagnetic compatibility (EMC) and safety standards as described in the Declaration of Conformity.
Changes that you make to the instrument might void compliance with one or more of these EMC and safety standards.
Changes to the instrument include replacing a part or adding components, options, or peripherals not specifically
authorized and qualified by Thermo Fisher Scientific. To ensure continued compliance with EMC and safety standards,
replacement parts and additional components, options, and peripherals must be ordered from Thermo Fisher Scientific
or one of its authorized representatives.
FCC Compliance Statement
THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES. OPERATION IS SUBJECT TO
THE FOLLOWING TWO CONDITIONS: (1) THIS DEVICE MAY NOT CAUSE HARMFUL
INTERFERENCE, AND (2) THIS DEVICE MUST ACCEPT ANY INTERFERENCE RECEIVED,
INCLUDING INTERFERENCE THAT MAY CAUSE UNDESIRED OPERATION.
CAUTION Read and understand the various precautionary notes, signs, and symbols contained inside
this manual pertaining to the safe use and operation of this product before using the device.
Notice on Lifting and Handling of

Thermo Scientific Instruments
For your safety, and in compliance with international regulations, the physical handling of this Thermo Fisher
Scientific instrument requires a team effort to lift and/or move the instrument. This instrument is too heavy and/or
bulky for one person alone to handle safely.
Notice on the Proper Use of
Thermo Scientific Instruments
In compliance with international regulations: This instrument must be used in the manner specified by Thermo Fisher
Scientific to ensure protections provided by the instrument are not impaired. Deviations from specified instructions on
the proper use of the instrument include changes to the system and part replacement. Accordingly, order replacement
parts from Thermo Fisher Scientific or one of its authorized representatives.
Notice on the Susceptibility

to Electromagnetic Transmissions
Your instrument is designed to work in a controlled electromagnetic environment. Do not use radio frequency
transmitters, such as mobile phones, in close proximity to the instrument.
For manufacturing location, see the label on the instrument.

Declaration of Conformity for the EASY-nLC II System
U.S. Safety and EMC (Electromagnetic Compliance) Standards

Safety
This instrument has been reviewed for compliance with standard ANSI/UL 3101-1, “Electrical Equipment for
Laboratory Use; Part 1: General Requirements,” 1st Edition.
EMC
This device complies with Part 15 of the FCC Rules. Operation is subject to the following two conditions:
1. This device may not cause harmful interference, and
2. This device must accept any interference received, including interference that may cause undesired operation.
WARNING Changes or modification to this unit not expressly approved by the party responsible for
compliance could void the user’s authority to operate the equipment.
Note
This equipment has been tested and found to comply with the limits for a Class A digital device, pursuant to Part
15 of the FCC Rules. These limits are designed to provide reasonable protection against harmful interference when
the equipment is operated in a commercial environment. This equipment generates, uses, and can radiate radio
frequency energy and, if not installed and used in accordance with the instruction manual, may cause harmful
interference to radio communications. Operation of this equipment in a residential area is likely to cause harmful
interference in which case users will be required to correct the interference at their own expense.
You must use shielded cables with this unit to ensure compliance with the Class A FCC limits.
Canadian Safety and EMC (Electromagnetic Compliance) Standards
Safety
This instrument has been reviewed for compliance with standard CAN/CSA-C22.2 No. 61010-1, Second edition -
“Safety Requirements for Electrical Equipment for Measurement, Control, and Laboratory Use; Part 1: General
Requirements.”
EMC
This Class A digital apparatus meets all requirements of the Canadian Interference-Causing Equipment Regulations.
European Safety and EMC (Electromagnetic Compliance) Standards
Application of Council 2006/95/EEC “Low Voltage”: Intertek Group plc

Directive(s)
89/336/EEC “Electromagnetic Compatibility”: DELTA Denmark
Standard(s) to which EN61010-1:2001, Second edition - “Safety Requirements for Electrical Equipment for
conformity is declared Measurement, Control and Laboratory Use”
EN61010-2-81 “Part 2-081: Particular requirements for automatic and semi-automatic

laboratory equipment for analysis and other purposes”
EN/(IEC) 61326-1:2006, A1(1998), A2(2001) and A3(2003) “EMC requirements for

electrical equipment for measurement, control and laboratory use”
Manufacturer’s Name Proxeon Biosystems A/S
Manufacturer’s Address Edisonsvej 4, DK-5000 Odense, Denmark
Type of Equipment Laboratory Instrumentation
Model Name EASY-nLC™ II
Model Numbers LC110/LC111
Serial Number LC-000100 and later
Year of Manufacture 2010–
I, the undersigned hereby declare that the equipment specified above conforms to the above Directive(s) and
Standard(s).
Ole Vorm, Site Manager August 31, 2010

Declaration of Conformity for the EASY-nLC 1000 System
U.S. Safety and EMC (Electromagnetic Compliance) Standards

Safety
This instrument has been reviewed for compliance with standard UL 61010-1, “Electrical Equipment for
Measurement, Control, and Laboratory Use; Part 1: General Requirements.”
EMC
This device complies with Part 15 of the FCC Rules. Operation is subject to the following two conditions:
1. This device may not cause harmful interference, and
2. This device must accept any interference received, including interference that may cause undesired operation.
WARNING Changes or modification to this unit not expressly approved by the party responsible for
compliance could void the user’s authority to operate the equipment.
Note
This equipment has been tested and found to comply with the limits for a Class A digital device, pursuant to Part
15 of the FCC Rules. These limits are designed to provide reasonable protection against harmful interference when
the equipment is operated in a commercial environment. This equipment generates, uses, and can radiate radio
frequency energy and, if not installed and used in accordance with the instruction manual, may cause harmful
interference to radio communications. Operation of this equipment in a residential area is likely to cause harmful
interference in which case users will be required to correct the interference at their own expense.
You must use shielded cables with this unit to ensure compliance with the Class A FCC limits.
Canadian Safety and EMC (Electromagnetic Compliance) Standards

Safety
This instrument has been reviewed for compliance with standard CAN/CSA-C22.2 No. 61010-1, Second edition -
“Safety Requirements for Electrical Equipment for Measurement, Control, and Laboratory Use; Part 1: General
Requirements.”
EMC
This Class A digital apparatus meets all requirements of the Canadian Interference-Causing Equipment Regulations.
European Safety and EMC (Electromagnetic Compliance) Standards
Application of Council 2004/108/EC “Electromagnetic Compatibility”
Directive(s) 2006/95/EC “Low Voltage Directive (LVD)”
Standard(s) to which IEC 61010-1: Second edition, 2001. Safety Requirements for Electrical Equipment for
conformity is declared Measurement, Control and Laboratory Use. Also conformity with
• EN 61010-1:2001
• UL 61010-1, second edition
• CAN/CSA-C22.2 No. 61010-1, Second Edition
EN/(IEC) 61326-1:2006. Electrical equipment for measurement, control and laboratory

use - EMC requirements - Part 1: General requirements
EN/(IEC) 61000-3-2:2006+A1+A2. Electromagnetic compatibility (EMC) - Part 3-2:

Limits - Limits for harmonic current emissions (equipment input current 16 A per phase)
EN/(IEC) 61000-3-3:2008. Electromagnetic compatibility (EMC) - Part 3-3: Limits -

Limitation of voltage changes, voltage fluctuations and flicker in public low-voltage supply
systems, for equipment with rated current 16 A per phase and not subject to conditional
connection
FCC CFR 47 Part 15, Class A. Radiated Emissions and Conducted Emissions
Manufacturer’s Name Proxeon Biosystems A/S
Manufacturer’s Address Edisonsvej 4, DK-5000 Odense, Denmark
Type of Equipment Laboratory Instrumentation
Model Name EASY-nLC™ 1000
Model Numbers LC120
Serial Number LC-010000 and higher
Year of Manufacture 2011–
I, the undersigned hereby declare that the equipment specified above conforms to the above Directive(s) and
Standard(s).
Ole Vorm, Site Manager July 19, 2011

WEEE Compliance
This product is required to comply with the European Union’s Waste Electrical & Electronic Equipment (WEEE)
Directive 2002/96/EC. It is marked with the following symbol:
Thermo Fisher Scientific has contracted with one or more recycling or disposal companies in each European Union
(EU) Member State, and these companies should dispose of or recycle this product. See www.thermoscientific.com/
rohsweee for further information on Thermo Fisher Scientific’s compliance with these Directives and the recyclers in
your country.
WEEE Konformität
Dieses Produkt muss die EU Waste Electrical & Electronic Equipment (WEEE) Richtlinie 2002/96/EC erfüllen.
Das Produkt ist durch folgendes Symbol gekennzeichnet:
Thermo Fisher Scientific hat Vereinbarungen mit Verwertungs-/Entsorgungsfirmen in allen EU-Mitgliedsstaaten

getroffen, damit dieses Produkt durch diese Firmen wiederverwertet oder entsorgt werden kann. Mehr Information
über die Einhaltung dieser Anweisungen durch Thermo Fisher Scientific, über die Verwerter, und weitere Hinweise,
die nützlich sind, um die Produkte zu identifizieren, die unter diese RoHS Anweisung fallen, finden sie unter
www.thermoscientific.com/rohsweee.
Conformité DEEE
Ce produit doit être conforme à la directive européenne (2002/96/EC) des Déchets d'Equipements Electriques et
Electroniques (DEEE). Il est marqué par le symbole suivant:
Thermo Fisher Scientific s'est associé avec une ou plusieurs compagnies de recyclage dans chaque état membre de
l’union européenne et ce produit devrait être collecté ou recyclé par celles-ci. Davantage d'informations sur la
conformité de Thermo Fisher Scientific à ces directives, les recycleurs dans votre pays et les informations sur les
produits Thermo Fisher Scientific qui peuvent aider la détection des substances sujettes à la directive RoHS sont
disponibles sur www.thermoscientific.com/rohsweee.
CAUTION Symbol CAUTION VORSICHT ATTENTION PRECAUCION AVVERTENZA
Electric Shock: This instrument uses Elektroschock: In diesem Gerät werden Choc électrique: L’instrument utilise des Descarga eléctrica: Este instrumento Shock da folgorazione. L’apparecchio è
high voltages that can cause personal Hochspannungen verwendet, die tensions capables d’infliger des blessures utiliza altas tensiones, capaces de alimentato da corrente ad alta tensione
injury. Before servicing, shut down the Verletzungen verursachen können. Vor corporelles. L’instrument doit être arrêté et producir lesiones personales. Antes de che puo provocare lesioni fisiche. Prima di
instrument and disconnect the instrument Wartungsarbeiten muß das Gerät débranché de la source de courant avant dar servicio de mantenimiento al effettuare qualsiasi intervento di
from line power. Keep the top cover on abgeschaltet und vom Netz getrennt tout intervention. Ne pas utiliser instrumento, éste debera apagarse y manutenzione occorre spegnere ed isolare
while operating the instrument. Do not werden. Betreiben Sie das Gerät nicht mit l’instrument sans son couvercle. Ne pas desconectarse de la línea de alimentacion l’apparecchio dalla linea elettrica. Non
remove protective covers from PCBs. abgenommenem Deckel. Nehmen Sie die enlever les étuis protecteurs des cartes de eléctrica. No opere el instrumento sin sus attivare lo strumento senza lo schermo
Schutzabdeckung von Leiterplatten nicht circuits imprimés. cubiertas exteriores quitadas. No remueva superiore. Non togliere i coperchi a
ab. las cubiertas protectoras de las tarjetas protezione dalle schede di circuito
de circuito impreso. stampato (PCB).
Chemical: This instrument might contain Chemikalien: Dieses Gerät kann Chimique: Des produits chimiques Química: El instrumento puede contener Prodotti chimici. Possibile presenza di
hazardous chemicals. Wear gloves when gefährliche Chemikalien enthalten. Tragen dangereux peuvent se trouver dans productos quimicos peligrosos. Utilice sostanze chimiche pericolose
handling toxic, carcinogenic, mutagenic, Sie Schutzhandschuhe beim Umgang mit l’instrument. Portez des gants pour guantes al manejar productos quimicos nell’apparecchio. Indossare dei guanti per
or corrosive or irritant chemicals. Use toxischen, karzinogenen, mutagenen oder manipuler tous produits chimiques tóxicos, carcinogenos, mutagenos o maneggiare prodotti chimici tossici,
approved containers and proper ätzenden/reizenden Chemikalien. toxiques, cancérigènes, mutagènes, ou corrosivos/irritantes. Utilice recipientes y cancerogeni, mutageni, o
procedures to dispose waste oil. Entsorgen Sie verbrauchtes Öl corrosifs/irritants. Utiliser des récipients procedimientos aprobados para corrosivi/irritanti. Utilizzare contenitori
entsprechend den Vorschriften in den et des procédures homologuées pour se deshacerse del aceite usado. aprovo e seguire la procedura indicata per
vorgeschriebenen Behältern. débarrasser des déchets d’huile. lo smaltimento dei residui di olio.
Heat: Before servicing the instrument, Hitze: Warten Sie erhitzte Komponenten Haute Temperature: Permettre aux Altas temperaturas: Permita que los Calore. Attendere che i componenti
allow any heated components to cool. erst nachdem diese sich abgekühlt haben. composants chauffés de refroidir avant componentes se enfríen, ante de efectuar riscaldati si raffreddino prima di
tout intervention. servicio de mantenimiento. effetturare l’intervento di manutenzione.
Fire: Use care when operating the system Feuer: Beachten Sie die einschlägigen Incendie: Agir avec précaution lors de Fuego: Tenga cuidado al operar el Incendio. Adottare le dovute precauzioni
in the presence of flammable gases. Vorsichtsmaßnahmen, wenn Sie das l’utilisation du système en présence de sistema en presencia de gases quando si usa il sistema in presenza di gas
System in Gegenwart von entzündbaren gaz inflammables. inflamables. infiammabili.
Gasen betreiben.
Eye Hazard: Eye damage could occur Verletzungsgefahr der Augen: Danger pour les yeux: Des projections Peligro par los ojos: Las salicaduras de Pericolo per la vista. Gli schizzi di
from splattered chemicals or flying Verspritzte Chemikalien oder kleine chimiques, liquides, ou solides peuvent productos químicos o particulas que prodotti chimici o delle particelle presenti
particles. Wear safety glasses when Partikel können Augenverletzungen être dangereuses pour les yeux. Porter des salten bruscamente pueden causar nell’aria potrebbero causare danni alla
handling chemicals or servicing the verursachen. Tragen Sie beim Umgang mit lunettes de protection lors de toute lesiones en los ojos. Utilice anteojos vista. Indossare occhiali protettivi quando
instrument. Chemikalien oder bei der Wartung des manipulation de produit chimique ou pour protectores al manipular productos si maneggiano prodotti chimici o si
Gerätes eine Schutzbrille. toute intervention sur l’instrument. químicos o al darle servicio de effettuano interventi di manutenzione
mantenimiento al instrumento. sull’apparecchio.
General Hazard: A hazard is present that Allgemeine Gefahr: Es besteht eine Danger général: Indique la présence Peligro general: Significa que existe un Pericolo generico. Pericolo non
is not included in the above categories. weitere Gefahr, die nicht in den d’un risque n’appartenant pas aux peligro no incluido en las categorias compreso tra le precedenti categorie.
Also, this symbol appears on the vorstehenden Kategorien beschrieben ist. catégories citées plus haut. Ce symbole anteriores. Este simbolo también se utiliza Questo simbolo è utilizzato inoltre
instrument to refer the user to instructions Dieses Symbol wird im Handbuch figure également sur l’instrument pour en el instrumento par referir al usuario a sull’apparecchio per segnalare all’utente
in this manual. außerdem dazu verwendet, um den renvoyer l’utilisateur aux instructions du las instrucciones contenidas en este di consultare le istruzioni descritte nel
Benutzer auf Anweisungen hinzuweisen. présent manuel. manual. presente manuale.
When the safety of a procedure is Wenn Sie sich über die Sicherheit eines Si la sûreté d’une procédure est Cuando la certidumbre acerca de un Quando e in dubbio la misura di sicurezza
questionable, contact your local Technical Verfahrens im unklaren sind, setzen Sie incertaine, avant de continuer, contacter procedimiento sea dudosa, antes de per una procedura, prima di continuare, si
Support organization for Thermo Fisher sich, bevor Sie fortfahren, mit Ihrer le plus proche Service Clientèle pour les proseguir, pongase en contacto con la prega di mettersi in contatto con il
Scientific San Jose Products. lokalen technischen produits de Thermo Fisher Scientific San Oficina de Asistencia Tecnica local para Servizio di Assistenza Tecnica locale per i
Unterstützungsorganisation für Thermo Jose. los productos de Thermo Fisher Scientific prodotti di Thermo Fisher Scientific San
Fisher Scientific San Jose Produkte in San Jose. Jose.
Verbindung.
CAUTION Symbol CAUTION
Electric Shock: This instrument uses

high voltages that can cause personal
injury. Before servicing, shut down the
instrument and disconnect the instrument
from line power. Keep the top cover on
while operating the instrument. Do not
remove protective covers from PCBs.
Chemical: This instrument might contain

hazardous chemicals. Wear gloves when
handling toxic, carcinogenic, mutagenic,
or corrosive or irritant chemicals. Use
approved containers and proper
procedures to dispose waste oil.
Heat: Before servicing the instrument,

allow any heated components to cool.
Fire: Use care when operating the system

in the presence of flammable gases.
Eye Hazard: Eye damage could occur

from splattered chemicals or flying
particles. Wear safety glasses when
handling chemicals or servicing the
instrument.
General Hazard: A hazard is present that

is not included in the above categories.
Also, this symbol appears on the
instrument to refer the user to instructions
in this manual.
When the safety of a procedure is

questionable, contact your local Technical
Support organization for Thermo Fisher
Scientific San Jose Products.
C
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xix
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xx
Downloading Manuals from the Customer Manuals Web Site . . . . . . . . . . . . . xx
Safety and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xxi
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xxiii
Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Hardware Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Solvent System Components Behind the Right Side Panel . . . . . . . . . . . . . . . 5
Computer and Autosampler Behind the Left Side Panel . . . . . . . . . . . . . . . . 15
Back Panel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Touch-Screen Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Description of the Touch-Screen Monitor. . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Logging In to the EASY-nLC Instrument for Maintenance Tasks . . . . . . . . . 20
Closing Down the EASY-nLC Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Specifications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Performance Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Technical Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Chapter 2 Maintenance Schedule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27

Daily Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Weekly Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Quarterly Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Yearly Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Field Service Repairs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Thermo Scientific EASY-nLC Series Troubleshooting and Maintenance Guide xiii

Contents
Chapter 3 Maintenance Scripts and Service Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .31

Maintenance Scripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Prepare – Purge Solvent. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Prepare – Flush Air . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Prepare – Precolumn Equilibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Prepare – Analytical Column Equilibration . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Prepare – Isocratic Flow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Test – MS Connection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Test – Sample Pickup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Test – Leaks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Test – Valve Check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Test – Back Pressure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Test – Autosampler Torque. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Test – Pump Torque . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Calibrate – Valve Tune . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Calibrate – Flow Sensors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Calibrate – Reset Pressure Sensor. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Calibrate – Direct Infusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Keeping Service Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Checking and Resetting the Device Usage Counters . . . . . . . . . . . . . . . . . . . . . 56
Chapter 4 Routine Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .57

Maintaining a Clean Working Environment . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Replacing the Main Power Fuse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Maintaining the Syringe Pumps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Retracting the Piston . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Replacing the Piston Seal and Cleaning the Piston in a PLF Pump . . . . . . . . 62
Replacing the Piston Seal in a PLU Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Priming the Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Resetting the Pump Usage Counter. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Removing Air After Replacing a Piston Seal or a Pump . . . . . . . . . . . . . . . . . 73
Running the Leaks Script after Replacing a Piston Seal or a Pump . . . . . . . . 73
Maintaining the Rotary Valves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Cleaning the Rotor Seal and Stator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Replacing the Rotor Seal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Replacing the Stator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Replacing the Check Valves. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Replacing an Inline Filter for the EASY-nLC 1000 Instrument . . . . . . . . . . . . . 81
Using nanoViper Fittings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Replacing the Autosampler Needle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Replacing the Sample Loop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Replacing a Pressure Sensor for the PLU Pump. . . . . . . . . . . . . . . . . . . . . . . . . 90
xiv EASY-nLC Series Troubleshooting and Maintenance Guide Thermo Scientific

Contents
Replacing a Flow Sensor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92

Replacing a Flow Sensor in the EASY-nLC 1000 Instrument . . . . . . . . . . . . 92
Replacing a Flow Sensor in the EASY-nLC II Instrument . . . . . . . . . . . . . . . 96
Replacing the Hard Drive . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
Managing the Devices List. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Chapter 5 Field Service Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .107

Replacing the Built-In Computer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
Replacing the Monitor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Replacing a Pressure Sensor for a PLF Pump . . . . . . . . . . . . . . . . . . . . . . . . . . 117
Replacing the ASC Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
Upgrading from an ASA Autosampler to an ASC Autosampler . . . . . . . . . . . . 128
Replacing the Autosampler Cooler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
Replacing the ASC Cooler. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
Replacing the ASA Cooler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
Replacing a Rotary Valve. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
Replacing a Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
Replacing a PLU Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
Replacing a PLF Pump with a PLU Pump. . . . . . . . . . . . . . . . . . . . . . . . . . 154
Replacing a Pump PCB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
Replacing a Pump PCB in the PLU Pump . . . . . . . . . . . . . . . . . . . . . . . . . 163
Replacing a Pump PCB in the PLF Pump . . . . . . . . . . . . . . . . . . . . . . . . . . 167
Chapter 6 Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .169

Troubleshooting Tips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
Autosampler Problems. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
Contact Closure Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
Instrument Startup Problems. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
Delayed Elution. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
Excessive Duration or Higher Pressure for the Column Equilibration
and Sample Loading Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
System Reaches Its Maximum Pressure During the Gradient. . . . . . . . . . . . 180
Sample Signal Weak or Absent . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
Slow or No Pressure Increase in Subsystem A or B . . . . . . . . . . . . . . . . . . . 187
Errors Reported by the Xcalibur Data System . . . . . . . . . . . . . . . . . . . . . . . 189
Carryover . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194
Spray Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
Chromatographic Performance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
Device Failures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
Miscellaneous . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202
Using the Direct Controls for Troubleshooting and Maintenance . . . . . . . . . . 204
Using the Valve Controls. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
Using the Pump Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205
Using the Autosampler Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 210
Thermo Scientific EASY-nLC Series Troubleshooting and Maintenance Guide xv

Contents
Troubleshooting a Pump that Fails the Flush Air Script . . . . . . . . . . . . . . . . . 212

Troubleshooting a Pump that Fails the Leaks Script . . . . . . . . . . . . . . . . . . . . 216
Running a System Leak Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218
Troubleshooting the Results of the System Leak Test . . . . . . . . . . . . . . . . . . . 221
Checking Valve S for a Leak . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222
Checking the Sample Loop Connections for a Leak. . . . . . . . . . . . . . . . . . . 222
Locating a Leak in the Solvent Path from Valve B to Flow Sensor B . . . . . . 223
Locating a Leak in the Solvent Path from Pump A to Flow Sensor
A . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224
Locating a Leak In or Between Valve S and Valve W. . . . . . . . . . . . . . . . . . 226
Locating a Leak Between the Flow Sensors and Valve S. . . . . . . . . . . . . . . . 234
Identifying a Leaking Check Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 248
Troubleshooting a System Blockage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249
Running the Back Pressure Test for the A and B Solvent Paths . . . . . . . . . . 250
Troubleshooting a System Blockage when Test Solvent A Fails . . . . . . . . . . 251
Troubleshooting a System Blockage when Test Solvent B Fails . . . . . . . . . . 257
Troubleshooting the Autosampler Aspiration and Calibration. . . . . . . . . . . . . 261
Checking Sample Pickup. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 263
Troubleshooting Communication Problems . . . . . . . . . . . . . . . . . . . . . . . . . . 264
Network Access . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 264
Network Connection Failures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265
Testing the Network Connection to the EASY-nLC Computer. . . . . . . . . . 266
Verifying that the LC/MS System Is Properly Grounded. . . . . . . . . . . . . . . . . 268
Chapter 7 Calibrating the Autosampler’s XYZ Robot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .269

Replacing the Autosampler Adapter Plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . 270
Replacing the Adapter Plate in the ASC Model Autosampler. . . . . . . . . . . . 271
Replacing the Adapter Plate in the ASA Model Autosampler . . . . . . . . . . . . 272
Managing Plate Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 274
Selecting a Plate Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 274
Creating a New Plate Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275
Deleting a Plate Format. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
Preparing the Autosampler for the Calibration Routines . . . . . . . . . . . . . . . . . 278
Calibrating Plates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 280
Calibrating the Wash Bottle and Extra Vial Positions . . . . . . . . . . . . . . . . . . . 285
Chapter 8 Remote Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .287

Connecting the EASY-nLC Instrument to the Support Server. . . . . . . . . . . . . 288
Saving System Files on a USB Removable Storage Device . . . . . . . . . . . . . . . . 293
Downloading the Latest Firmware File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 296
Chapter 9 Returning the EASY-nLC Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .299

Transport Instructions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 299
Declaration of Contamination. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301
xvi EASY-nLC Series Troubleshooting and Maintenance Guide Thermo Scientific

Contents
Appendix A Error Codes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .303
Appendix B Mobile Phase Viscosity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .311
Appendix C Consumables and Replacement Parts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .313

Ordering Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 313
Solvent System Schematic for the EASY-nLC II Instrument . . . . . . . . . . . . . . 314
Solvent System Schematic for the EASY-nLC 1000 Instrument . . . . . . . . . . . 316
Common Replacement Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 318
Common Replacement Parts for the EASY-nLC II Instrument . . . . . . . . . . 318
Common Replacement Parts for the EASY-nLC 1000 Instrument . . . . . . . 319
Appendix D Quick Reference Guides for Routine Maintenance . . . . . . . . . . . . . . . . . . . . . . .321

Using nanoViper Fittings Quick Reference Guide. . . . . . . . . . . . . . . . . . . . . . 323
Connecting nanoViper Fittings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 323
nanoViper Tubing Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 324
Returning the System to Atmospheric Pressure . . . . . . . . . . . . . . . . . . . . . . 325
Maintaining the PLU Pump Quick Reference Guide . . . . . . . . . . . . . . . . . . . 327
Maintaining the PLF Pump Quick Reference Guide . . . . . . . . . . . . . . . . . . . . 329
Maintaining the Rotary Valves Quick Reference Guide. . . . . . . . . . . . . . . . . . 331
Replacing a Damaged Autosampler Needle . . . . . . . . . . . . . . . . . . . . . . . . . . . 333
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .335
Thermo Scientific EASY-nLC Series Troubleshooting and Maintenance Guide xvii

P
Preface
This guide describes the maintenance and troubleshooting procedures required to maintain
the EASY-nLC™ instrument in optimal working condition.
The hardware maintenance procedures are divided into two chapters: Routine Maintenance
and Advanced Maintenance. The Routine Maintenance chapter contains common
maintenance procedures that you can perform to keep the EASY-nLC instrument in optimal
working condition. The Advanced Maintenance chapter contains hardware repair procedures
that can only be performed by a Thermo Fisher Scientific field service engineer or a skilled
technician with equivalent training.
For information about setting up the EASY-nLC instrument and running chromatographic
separations, refer to the EASY-nLC Series Getting Started Guide.
Contents
• Related Documentation
• Downloading Manuals from the Customer Manuals Web Site
• Safety and Special Notices
• Contacting Us
 To suggest changes to documentation or to Help
If you are viewing a PDF file of this manual online, complete a brief survey about this
document by clicking the button below.
If you are reading a printed copy of this manual, complete a brief survey about this
document by going to the following URL.
http://www.surveymonkey.com/s/PQM6P62
Thermo Scientific EASY-nLC Series Troubleshooting and Maintenance Guide xix

Preface
Related Documentation
In addition to this guide, Thermo Fisher Scientific provides the following documents for the
EASY-nLC instrument:
• EASY-nLC Series User Guide for the Xcalibur 2.x Data System
• EASY-nLC Preinstallation Requirements Guide
• EASY-nLC Series Getting Started Guide
Downloading Manuals from the Customer Manuals Web Site

For Thermo Scientific software and hardware products, Thermo Fisher Scientific provides
instructional guides as PDF files on its Customer Manuals Web site.
Note If you are using a Thermo Scientific application to control the EASY-nLC system as
part of an LC/MS system, the EASY-nLC manuals are also available from the data system
computer’s Start menu.
 To download the EASY-nLC manuals from the Customer Manuals Web site
1. Go to mssupport.thermo.com.
2. On the Terms and Conditions page, click I Agree.
3. Click Customer Manuals in the left margin of the window.
4. On the right side of the window, click Search.
The Documents - Advanced Search page opens.
5. Open a list of linked PDF documents for the EASY-nLC as follows:

a. In the Model list, select EASY-nLC and in the Document Type list, select Manual.
b. Click Submit Search.
xx EASY-nLC Series Troubleshooting and Maintenance Guide Thermo Scientific

Preface
6. On the Documents page, click the link to the right of Download to view the PDF.
7. Click the Save a Copy icon, , browse to an appropriate folder, and then click Save to
save a copy of the document.
Safety and Special Notices

Make sure to follow the safety practices presented in this guide, and observe the safety and
special notices that appear in boxes.
Observe all written safety precautions during all phases of operation, service, and repair of this
instrument. Failure to comply with these precautions or with specific warnings elsewhere in
this manual violates safety standards of design, manufacture, and intended use of the
instrument and might result in injury or loss of life.
The following two stickers appear on the EASY-nLC instrument:
This sticker warns you that the instrument includes a sharp needle and moving parts that are
accessible to the operator. To prevent personal injury or damage to parts of the EASY-nLC
instrument, take care when loading samples into the instrument’s tray compartment.
WARNING: SHARP NEEDLE AND MOVING PARTS.

KEEP HANDS CLEAR.
AIGUILLE POINTURE ET PARTIES MOUVANTES.
AVERTISSEMENT:
TENIR LES MAINS A` L’ECART
´
This sticker alerts you to consult this manual for instructions on how to operate the
instrument.
The safety and special notices in the documentation include the following:
CAUTION Highlights hazards to humans, property, or the environment. Each CAUTION

notice is accompanied by an appropriate CAUTION symbol.
CAUTION Highlights electrical hazards to humans or property.
Thermo Scientific EASY-nLC Series Troubleshooting and Maintenance Guide xxi

Preface
CAUTION Highlights a sharp object hazard to humans.
CAUTION Highlights an eye hazard to humans.
CAUTION Highlights a chemical hazard to humans, property, or the environment.
CAUTION Highlights lifting hazards.
IMPORTANT Highlights information necessary to prevent damage to software, loss of

data, or invalid test results; or might contain information that is critical for optimal
performance of the system.
Note Highlights information of general interest.
Tip Highlights helpful information that can make a task easier.
xxii EASY-nLC Series Troubleshooting and Maintenance Guide Thermo Scientific

Preface
Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need.
 To contact Technical Support for the EASY-nLC instrument
Web site www.proxeon.com

E-mail (North and South America)
us.customer-support.analyze@thermofisher.com
(Other continents)
eu.techsupport.cmf@thermofisher.com
Address Thermo Fisher Scientific
Edisonvej 4
DK-5000 Odense C
Find software updates and utilities to download at mssupport.thermo.com.
 To order consumable and spare parts for the EASY-nLC instrument

For the EASY-nLC 1000 instrument, go to:
www.proxeon.com/productrange/nano_lc_easy-nlc_1000/accessories_spares/index.html
For the EASY-nLC II instrument, go to:
www.proxeon.com/productrange/nano_lc/accessories-spares/index.html
Thermo Scientific EASY-nLC Series Troubleshooting and Maintenance Guide xxiii

1
Introduction
The EASY-nLC instrument (see Figure 1) consists of a high-pressure dual pump
chromatography system that provides split-free flows down to the low nanoLiter/min range,
an automated sampling system, and a built-in computer with a touch-screen interface for
instrument control and troubleshooting. The automated sampling system includes a tray
compartment that can hold standard sample vials and microtiter plates, an XYZ robot that
moves to the sample location, and a syringe pump that draws only the user-specified sample
volume.
The EASY-nLC II instrument operates in the high-performance pressure range of 1 to

300 bar and the EASY-nLC 1000 instrument operates in the ultra-high-performance pressure
range of 1 to 1000 bar.
Figure 1. EASY-nLC II instrument on the left and EASY-nLC 1000 instrument on the right
To familiarize yourself with the EASY-nLC instrument and its instrument control software,
review these topics.
Contents
• Hardware Components
• Touch-Screen Application
• Specifications
Note For information about setting up the EASY-nLC instrument, installing the
columns, creating methods, and running batches, refer to the EASY-nLC Series Getting
Started Guide.
Thermo Scientific EASY-nLC Series Troubleshooting and Maintenance Guide 1

1 Introduction
Hardware Components
Hardware Components
These topics describe the hardware components of the EASY-nLC instrument:
• Autosampler
• Solvent System Components Behind the Right Side Panel
• Computer and Autosampler Behind the Left Side Panel
• Back Panel
Autosampler
The autosampler module of the EASY-nLC instrument is located behind the tray
compartment door. You can open the tray compartment door manually or by using the
touch-screen controls.
With the use of a vial adapter plate or a microwell adapter plate, the tray compartment can
hold sample vials, a 96-well microplate, or a 384-well microplate.
The robotic unit moves the z-axis needle holder along the x and y axes to the user-specified
sample location during a run. When the autosampler needle reaches the sample location, it
descends into the sample vial or microplate well.
IMPORTANT Because they can block the movement of the z-axis needle holder, avoid
placing tall objects into the tray compartment.
The autosampler needle draws solvent from wash bottle W3 to perform a standard wash and
ejects the solvent into wash bottle W4, which contains the needle wash insert. The
autosampler can also perform a custom wash using the solvents from wash bottles W1–W3.
The waste beaker to the right of the tray compartment collects solvent that is delivered by
pumps A and B when these pumps empty solvent to waste. This waste beaker also collects
solvent delivered by pump A during the precolumn equilibration and sample loading steps
(for a two-column setup).
The EASY-nLC Series includes two supported versions of the autosampler module:
• “ASC Model—Current” on page 3
• “ASA Model—Legacy EASY-nLC II Instruments” on page 4
Note The ASC model has an integrated cooling compartment, which ensures stable
temperature conditions throughout the entire vial plate. By contrast, the ASA model is
cooled from underneath only.
2 EASY-nLC Series Troubleshooting and Maintenance Guide Thermo Scientific

1 Introduction
Hardware Components
The following differences between the two autosampler models affect the routine calibration
and maintenance procedures:
• The z-axis needle holders and the autosampler needles. This difference affects the
autosampler needle replacement procedure.
• The location of the wash bottles. This difference affects the autosampler calibration
procedure.
• The adapter plate holder. The adapter plate holder for the ASC model holds an additional
six sample vials. This difference affects the autosampler calibration procedure and the
maximum number of sample vials that you can run without reloading the autosampler.
ASC Model—Current
Figure 2 shows the ASC autosampler model that is installed in the current versions of the
EASY-nLC II and EASY-nLC 1000 instruments.
Figure 2. ASC autosampler model installed in the current versions of the EASY-nLC instruments
y axis (left and right)
z-axis
needle holder
Sample vial tray
x axis (in and out)

1 Introduction
Hardware Components
Figure 3 shows the tray compartment for the ASC autosampler as viewed from above when
the tray compartment door is open. The tray compartment of the ASC autosampler model
holds a vial adapter or a well plate adapter, six additional vials, three wash solvent bottles, and
a wash bottle with a wash insert for cleaning the autosampler needle.
Figure 3. Tray compartment for the ASC autosampler model (viewed from above)
Well plate (96 or 384) Three positions for Waste bottle with wash Six extra vial positions for
or vial (6 × 8) adapter wash solvents insert for cleaning of the standards or regular
outside of the needle samples
ASA Model—Legacy EASY-nLC II Instruments

Figure 4 shows the ASA autosampler model that is installed in earlier versions of the
EASY-nLC II instrument.
Figure 4. ASA autosampler model installed in earlier versions of the EASY-nLC II instrument
y axis (left and right)
z-axis needle holder
Adapter plate holder

with peltier cooling
Wash
bottles
x axis (in and out)

1 Introduction
Hardware Components
Figure 5 shows the tray compartment for the ASA autosampler model as viewed from above
when the tray compartment door is open. The tray compartment of the ASA autosampler
model holds a vial adapter or a well plate adapter, three wash solvent bottles, and a wash bottle
with a wash insert for cleaning the autosampler needle. The ASA autosampler model does not
hold six additional vials.
Figure 5. Tray compartment for the ASA autosampler model (viewed from above)
Solvent System Components Behind the Right Side Panel

The EASY-nLC solvent delivery system is located behind the right side panel and consists of
three syringe pumps, three pressure sensors, two flow sensors, four rotary valves, four check
valves (two for each assembly), and a mixing Tee.
Note Two of the syringe pumps (pumps A and B) produce the binary mobile phase and
the third syringe pump (pump S) draws the sample into the sample loop that is attached
to one of the rotary valves (valve S).
These topics describe the hardware components behind the right side panel:
• View Behind the Right Side Panel
• Syringe Pumps
• Pressure Sensors
• Flow Sensors
• Check Valve Assemblies
• Six-Port Rotary Valves
• Autosampler Needle
View Behind the Right Side Panel

You can access the solvent system components by removing the instrument’s right side panel,
which is secured to the housing with three captive quarter-turn screws.

1 Introduction
Hardware Components
Figure 6 shows the EASY-nLC II solvent system.

Figure 6. Solvent system components behind the right panel of the EASY-nLC II instrument
Mixing Tee
Solvent A
check valve
Autosampler assembly
needle
Waste In Solvent B
line check valve
assembly
Valve W Valve S Valve A Valve B
1 1 1 1
6
6
2
2
Rotary
5
5
3
3
4 4 4 4 valves
W, S, A, and B
Column Out
line + Pressure
–
sensors
S, A, and B
Flow sensors
A and B
Pump S Pump A Pump B
Pumps
S, A, and B

1 Introduction
Hardware Components
Figure 7 shows the solvent system components for the EASY-nLC 1000 instrument.
Figure 7. Solvent system components behind the right panel of the EASY-nLC 1000 instrument
Solvent A
check valve Solvent B
assembly check valve
assembly
Autosampler needle
Four 3-position,
6-port valves
Pressure sensor S
Mixing Tee
Pressure
sensors
A and B
Three syringe
pumps
Flow sensors
A and B

1 Introduction
Hardware Components
Syringe Pumps
The EASY-nLC instrument contains three syringe pumps. The binary liquid chromatography
system consists of two high-pressure pumps: pumps A and B. The automated sampling system
uses syringe pump S to draw sample from a sample vial or well and load it into the sample
loop attached to valve S.
Figure 8 shows the EASY-nLC syringe pump components. The PLF model is installed in the
EASY-nLC II instrument. The PLU model is installed in the EASY-nLC 1000 instrument and
is supplied as spare part for both instruments.
Each syringe pump consists of these primary components: a stepper motor, a pump body, a
pump head, a piston, a piston seal, and a backup ring. The PLU model also has an LED panel
and a pump printed circuit board (PCB) cover. The piston seal is the only user-replaceable
component.
The pump head holds up to 140 μL of fluid. The backward movement of the piston draws
solvent into the pump head and the forward movement of the piston pushes solvent into the
attached high-pressure solvent line. The stepper motor controls the forward and backward
movement of the piston within the pump head. The pump body provides piston alignment.
The piston seal allows the piston to move freely within the pump head. The piston seal is
made of an extremely strong thermoplastic. The seal for the EASY-nLC 1000 pumps contains
a wire spring that forces the inside flange of the seal against the piston to prevent leaks. The
seals are not leak proof. In fact, wetting the surface of the pistons requires a small quantity of
liquid, which acts as a lubricant to reduce wear on the piston seal. Through continued use and
over time, the seal degrades and must be replaced. Allowing the pump to run dry and
neglecting to rinse the pump head assemblies after pumping buffered eluents shorten the
lifespan of the seals.
The backup ring holds the piston seal in place. It also provides better alignment of the piston.

1 Introduction
Hardware Components
Figure 8. Syringe pump components (showing the pump head removed from the pump body)
EASY-nLC II syringe pump (PLF model) EASY-nLC 1000 syringe pump (PLU model)
Pump head
Piston seal
Piston
Backup ring Backup ring
LED
panel
Rotary switch
Pump body
Stepper motor
Motor cable
The syringe pumps perform these functions.
Component Function
Pumps A and B Draw solvent from the solvent bottles on top of the instrument, empty
solvent to the waste beaker, and deliver solvent to the mixing Tee.
Pump S Draws solvent from the W3 bottle, draws sample from the specified
sample location into the autosampler needle, and empties solvent to
the W4 bottle in the autosampler tray compartment.
For maintenance purposes, the system tracks the volume pumped by each pump
(see “Checking and Resetting the Device Usage Counters” on page 56).
The PLF model pumps installed in the EASY-nLC instrument have an error LED. The LED
illuminates green when the instrument is turned on and the pump is functioning properly.

1 Introduction
Hardware Components
The LED panels for the PLU model pumps installed in the EASY-nLC 1000 instrument
provide the following status information.
LED States
Flow sensor for Illuminates blue—the instrument is turned on and the flow sensor is
Pumps A and B connected to the pump.
Not illuminated—the instrument is not turned on or the flow sensor
is not connected to the pump.
Power Illuminates yellow—The instrument power is turned on.
Not illuminated—The instrument power is turned off.
Error Illuminates red—A pump error has occurred.
Not illuminated—The pump is operating properly.
Pressure Sensors
For pumps A, B, and S, the three pressure sensors connect the solvent path between the pump
outlet and the associated rotary valve.
Using the strain gauge principle to measure pressure accurately, the pressure sensors are
flow-through, zero dead volume devices with a wetted path that contains 12 μL of
swept volume. The pressure sensors for the EASY-nLC II instrument have an operating range
of 0 to 5000 psi (345 bar), and the pressure sensors for the EASY-nLC 1000 instrument have
an operating range of 0 to 15 000 psi (1034 bar).
Flow Sensors
The two flow sensors provide feedback control for pumps A and B. The flow sensors are
liquid mass flow meters with a CMOSens™ patented technology. Each flow meter consists of a
length of fused silica capillary, a sensor chip, a heating resistor, and two temperature sensors
(see Figure 9).
Figure 9. Flow sensor schematic
Flow Tubing
Heater
Temperature sensors
Sensor chip Based on CMOSens™ Technology
Principle patented: US Pat. 6 813 944

1 Introduction
Hardware Components
The flow sensors determine the flow rate of solvents passing through the system by measuring
the heat transfer through the fused silica capillary. Outside the capillary, a heating resistor on a
thermally optimized membrane is maintained above ambient temperature. When liquid flows
through the capillary, the temperature distribution upstream and downstream of the heating
resistor is disturbed. The two temperature sensors measure this temperature asymmetry.
Because the temperature distribution depends on both the solvent flow rate and the solvent
mixture, you must recalibrate the flow sensors whenever you change the solvent types for
solvents A and B. For example, if you use methanol instead of acetonitrile for the solvent B
mixture, run the script “Calibrate – Flow Sensors” on page 51.
The EASY-nLC 1000 instrument uses two flow sensors with a maximum measuring
range of 5.0 μL/min. The EASY-nLC II instrument uses two different flow sensors. The
maximum measuring range is approximately 2.9 μL/min for flow sensor A and 4.5 μL/min
for flow sensor B.
The wetted path for the EASY-nLC 1000 instrument includes external inline filters for the
flow sensor inlets and outlets. When the inline filters become clogged, they must be replaced.
For the EASY-nLC II instrument, the tubing that connects the valve to the flow sensor
contains a built-in filter.
Check Valve Assemblies

When the corresponding high-pressure (6-port rotary) valves for pumps A or B are in
position 1–2, the check valves perform these functions:
• The solvent-side check valve prevents backflow into the associated solvent inlet line when
the associated pump is emptying solvent to the waste beaker.
• The waste-side check valve prevents backflow from the waste beaker when the associated
pump is filling and drawing solvent from the associated solvent bottle.
Figure 10. Check valve connections
From the solvent reservoir bottle Solvent-side
on the top of the instrument check valve
Connected to
port 2 of
valve A or B
Waste-side
check valve
Routed to the waste beaker
The check valves are replaceable. For more information about determining if the check valves
are leaking, see “Identifying a Leaking Check Valve” on page 248.

1 Introduction
Hardware Components
Six-Port Rotary Valves

The three-position, six-port rotary valves consist of a driver, a rotor seal, and a stator (see
Figure 11).
Figure 11. Valve components
Driver
Rotor seal
Stator
Screws that
secure the stator
to the driver
The six-port valves can be in three different positions: 1–2 position, 1–6 position, and
centered (see Figure 12).
Figure 12. Valve positions
1–2 position 1–6 position Centered
1 1
2 6 2 6
3 4 5 3 4 5
For maintenance purposes, the system tracks the number of valve shifts for each valve
(see “Checking and Resetting the Device Usage Counters” on page 56).
Depending on the valve position, the valves perform the functions listed in Table 1.
Note The EASY-nLC solvent system contains three subsystems, one for each pump.
A subsystem includes the pump, the pressure sensor, the solvent lines to and from the
pressure sensor, and the rotary valve.

1 Introduction
Hardware Components
Table 1. Valve functions

Component Function
Valves A and B Direct the solvent flow from syringe pump A and B, respectively.
1–2 position Directs the solvent flow toward the check valve. When
the valve is in the 1–2 position, the pump draws solvent
from the solvent bottle on top of the instrument or
empties solvent to the waste beaker.
1–6 position Directs the solvent flow toward the mixing Tee.
Centered • Prevents backflow into the solvent line upstream of
the mixing Tee.
• Allows the back pressure for the solvent A and B lines
to equalize before the gradient step of a sample run.
• Blocks the solvent path through the valve and to the
subsystem for several maintenance scripts.
Valve S Directs the solvent flow from syringe pump S and the solvent flow from
the mixing Tee.
1–2 position The solvent flow bypasses the sample loop.
1–6 position The solvent flow passes through the sample loop.
Centered • Isolates the pump S subsystem for the Flush Air
script.
• Blocks the solvent path after valve S for the system
leak test (Leaks script with the System check box
selected).
• Shuts off the flow to the Column Out line and
provides back pressure during the Flow Sensor
Calibration script.
Valve W Directs the solvent flow through the venting Tee to the waste beaker or
provides pressure venting to the system.
1–2 position Directs the solvent flow toward the column by blocking
the solvent path through valve W.
1–6 position Directs the solvent flow from the venting Tee to the waste
beaker.
Centered Blocks the solvent flow through the valve to the waste
beaker.

1 Introduction
Hardware Components
Autosampler Needle
During a sample run, the autosampler needle descends into the requested sample vial or well,
and then pump S draws the requested sample volume into the needle tubing. The
autosampler needle is a user-replaceable part. For information about replacing the
autosampler needle, see “Replacing the Autosampler Needle” on page 84.
The autosampler needle for the ASC autosampler is a length of PEEKsil™ tubing with a sleeve
and a stainless steel fitting at one end and a PEEK™ nut and plastic stop at the other end
(see Figure 13). Fitting into a slot in the panel between the solvent system compartment and
the tray compartment, the needle retainer properly positions the needle tubing.
Figure 13. Autosampler needle for the ASC autosampler (current EASY-nLC II and EASY-nLC 1000
instruments)
Stainless steel fitting

and sleeve
Needle PEEK nut

retainer
Plastic stop
Figure 14 shows autosampler needle for the ASA autosampler.

Figure 14. Autosampler needle for the ASA autosampler model (earlier EASY-nLC II instruments)
For both needles, the stainless steel fitting connects to port 1 of valve S. The tubing routes
through a cutout in the panel that separates the solvent delivery system components from the
autosampler compartment. The other end of the tubing slides into the z-axis holder and is
secured with a PEEK nut.

1 Introduction
Hardware Components
Computer and Autosampler Behind the Left Side Panel

You can access the integrated computer and the autosampler needle fitting that connects to
the needle guide by removing the left side panel of the instrument (see Figure 15). Three
captive quarter-turn screws secure the left side panel to the instrument housing.
Figure 15. Internal features (behind the left side panel)
Integrated
computer
Needle tubing
Needle guide
Autosampler
Enclosed refrigerated
sample compartment

1 Introduction
Hardware Components
Back Panel
The system communication, contact closure, and power line connections are on the back
panel of the instrument (see Figure 16 and Figure 17).
Figure 16. Back panel of the EASY-nLC instrument (prior to March 2012)
PRO E O N
P-BUS
IN3 OUT3 IN2 OUT2 IN1 OUT1

PS/2 LAN MONITOR
HARD
DRIVE
This device complies with Part 15 of the FCC Rules. I

Operation is subject to the following two conditions:
(1) This device may not cause harmful interference, and O
(2) This device must accept any interference received, including
interference that may cause undersired operation.
This instrument is for research use only.
DEVICE: EASY-NLC 110-120V▼
P/N LC100
LAN MAC ADDRESS: 00-6--E0-45-4E-28 220-240▼
Proxeon Biosystems A/S 120/230 V : 50/60 Hz: 250 W

Web: www.proxeon.com Fuse at 120 V– : T5 AL 250 V
Fuse at 230 V– : T2.5 AL 250 V
Phone +45 6557 2300 Fax +45 6557 2301
Figure 17. Back panel of the EASY-nLC instrument (with the latest computer box)
P-BUS
USB LAN RS-232 MONITOR
HARD
DRIVE
This device complies with Part 15 of the FCC Rules. I

(1) This device may not cause harmful interference, and O
(2) This device must accept any interference received, including
interference that may cause undersired operation.
DEVICE: EASY-NLC 110-120V▼
P/N LC100
Thermo Fisher Scientific A/S 120/230 V : 50/60 Hz: 250 W

Web: www.proxeon.com Fuse at 120 V– : T5 AL 250 V
Fuse at 230 V– : T2.5 AL 250 V
Phone +45 6557 2300 Fax +45 6557 2301

1 Introduction
Hardware Components
Table 2 lists the function of each back panel element.

Table 2. Back panel elements
Element Description
RS-232 For communication with add-on devices, for example a syringe
drive
USB Port for keyboard or mouse or removable USB storage device,
two (2) provided
PS/2 (discontinued Input for connection of keyboard and mouse
computer box only)
LAN For 10/100 MB/sec Ethernet connection
MONITOR Output for connection of external display
P-BUS For communication with add-on devices
IN/OUT pins Contact closure (primarily for communication with the mass
spectrometer)
I|O Power switch
Fuse holder below Replaceable fuse ratings:

I|O switch
• For 120 V, T 5 AL, 250 V
• For 230 V, T 2.5 AL, 250 V
P/N Product order code
S/N Instrument serial number
LAN MAC ADDRESS MAC address of the embedded computer (Gives the EASY-nLC
computer a unique network identifier on your local network.)

1 Introduction
Touch-Screen Application
The EASY-nLC instrument includes an integrated computer with instrument control
software that you access from the instrument monitor.
These topics provide an overview of the touch-screen application and describe how to log in
to the EASY-nLC instrument as an administrator and how to close down the instrument:
• Description of the Touch-Screen Monitor
• Logging In to the EASY-nLC Instrument for Maintenance Tasks
• Closing Down the EASY-nLC Instrument
Description of the Touch-Screen Monitor

The instrument monitor is a transparent layer of glass that detects finger pressure (even while
wearing gloves) and sends the corresponding commands to the computer (see Figure 18).
Figure 18. Touch-screen controls
Home > Overview page

1 Introduction
Instrument control from this touch-screen application includes a method wizard that helps
you create chromatographic methods, a batch editor that helps you create and run sample
batches (injection sequences); maintenance scripts and record keeping features; and direct
control of the valves, pumps, XYZ robot, and tray temperature.
Note This guide describes how to log in to the instrument as an administrator, how to use
the maintenance scripts and record keeping features, and how to exit the touch-screen
application in a controlled manner and turn off the instrument before performing
maintenance procedures on the instrument’s hardware components.
For information about the maintenance scripts and record keeping features, see
Chapter 3, “Maintenance Scripts and Service Records.” For information about creating
methods and sample batches and running sample batches, refer to the EASY-nLC Series
Getting Started Guide (for the touch-screen application).
The EASY-nLC touch-screen application contains five menu tabs at the top of the
touch screen. When you press a tab at the top of the touch screen, a set of side tabs appears
on the left side of the touch screen. Figure 19 shows the menu layout for the Home >
Overview page.
Figure 19. EASY-nLC touch screen with the menu layout on the Home > Overview page
Top menu tabs
Logo icon
Side tabs
Current user
Login and Exit button

1 Introduction
During a session, the application tracks which page (side tab) you chose inside each menu
(top tab) and shows that page when you next choose that menu.
The Thermo Scientific logo icon in the upper left corner and the Login button in the lower
left corner are always available.
To view the version information for the application, press the Logo icon.
Logging In to the EASY-nLC Instrument for Maintenance Tasks

To run the maintenance scripts, use the direct controls, set up the system configuration, and
so on, you must log in to the EASY-nLC instrument as an administrator.
 To log in as a user with administrative privileges
1. Press Login in the lower left corner of the touch screen (see Figure 19 on page 19).
The Login As User dialog box opens (see Figure 20).
Figure 20. Login As User dialog box
2. In the User list, select a user with administrative rights.

3. In the Password box, enter the password for this user.
Tip The factory user name and password for the system administrator is admin.

1 Introduction
4. Press Accept.
Figure 21. EASY-nLC login dialog box
Closing Down the EASY-nLC Instrument

Closing down the instrument in a controlled manner is important to allow all of the
components to shut down in an orderly sequence. Using this controlled method saves
important data so that the instrument starts with the correct information the next time
you use it.
IMPORTANT If you turn off the power switch during normal operation, you risk
damaging essential system components.
 To close down the EASY-nLC instrument and turn off the power
1. Press Exit (lower-left corner of the screen).

A confirmation dialog box opens (see Figure 22).
Figure 22. Confirmation dialog box that opens after pressing Exit

1 Introduction
2. Press Power Down.

The EASY-nLC application displays a white screen with a small progress bar. When the
progress bar is filled out and the message appears indicating you can safely turn off the
instrument, go to the next step.
3. After receiving the message that you can safely turn off the instrument, turn off the power
switch on the back panel of the instrument.

1 Introduction
Specifications
Specifications
These topics describe the performance and technical specifications for the EASY-nLC syringe
pumps and autosampler:
• Performance Specifications
• Technical Specifications
Performance Specifications
Table 3 lists the performance specifications for the EASY-nLC instruments.
Table 3. Performance specification (Sheet 1 of 2)
Item Specification
Flow range (gradient) 20 to 2000 nL/min
Recommended: 100 to 1000 nL/min
Flow while loading and Up to 25 μL/min
equilibrating
Pressure range EASY-nLC II: 0 to 300 bar
EASY-nLC 1000: 0 to 1000 bar
Retention time Within the recommended flow range: 0.1 to 0.4%
reproducibility (RT RSD) Outside the recommended flow range: typically better
than 1%
Peak widths Typically 3 to 5 seconds full width at half maximum (fwhm),
using PepMap™ nano-bore columns as supplied at delivery
Carryover Typically < 0.05%
Conditions: Injection of 100 fmol tryptic digests of BSA on
Pepmap columns as supplied at delivery and by using the
standard wash procedure for the autosampler
Autosampler sample pickup 0.1 to 18 μL with the standard 20 μL loop
volume range 0.1 to 48 μL with a 50 μL loop
Injection reproducibility 0.2% at 5 μL pickup
(injection RSD) 3.0% at 0.1 μL pickup
Injection linearity 0.9985 at 0.5 to 10 μL injection volume

1 Introduction
Specifications
Table 3. Performance specification (Sheet 2 of 2)

Item Specification
Autosampler formats
ASC model 6 × 8 Vials + 6 Vials
1 × 96 well MTP + 6 Vials
1 × 384 well MTP + 6 Vials
2 × 48 PCR strips + 6 Vials
4 × 24 PCR strips + 6 Vials
ASA model 6 × 8 Vials
(earlier versions of the 1 × 96 well MTP
EASY-nLC II 1 × 384 well MTP
instrument) 2 × 48 PCR strips
4 × 24 PCR strips
Autosampler cooling 20 °C below ambient, typical setting: 7 °C (45 °F)
Technical Specifications
These tables list the technical specifications for the EASY-nLC instrument:
• General specifications, Table 4
• Physical specifications, Table 5
• Electrical specifications, Table 6
• Communication specifications, Table 7
• Hardware components, Table 8
Table 4. General specifications
Item Specification
Sound pressure level < 70 dBA
Operating temperature 5 to 30 °C
Storage temperature –25 to +60 °C
Humidity 20 to 80% RH, non-condensing
Sample viscosity 0.1 to 5 cP
Solvent A Water with 0.1% formic acid
Solvent B Acetonitrile with 0.1% formic acid
Note Use only LC/MS-grade solvents
Safety According to IEC 61010

1 Introduction
Specifications
Table 5. Physical specifications

Item EASY-nLC II EASY-nLC 1000
Width 35 cm (13.8 in.) 36 cm (14.2 in.)
Depth 38 cm (15.1 in.) 38 cm (15.1 in.)
Height 45 cm (17.7 in.) 45 cm (17.7 in.)
Weight 32 kg (70.5 lb) 35 kg (77 lb)
Weight in the shipping 45 kg (99 lb) 45 kg (99 lb)
container
Table 6. Electrical specifications

Item Specification
Power requirements 120 Vac, 50/60 Hz, 250 W
230 Vac, 50/60 Hz, 250 W
For universal power supply (UPS) dimensioning, assume 250 W.
Fuses For 120 Vac: one T 5 AL 250 V fuse (5 × 20 mm, IEC 60127)
For 230 Vac: one T 2.5 AL 250 V fuse
All fuses are UL Listed and CSA certified.
Table 7. Communication specifications

Item Specification
Contact closure 3 outputs, 3 inputs, and 6 ground pins
IN circuit TTL Level
OUT circuit PhotoMOS™ relay protected against high voltages. Continuous
switch current from 0.8 to 5 V is 35 mA.
LAN 10/100 Mb/s BaseT Ethernet
USB 2 × USB 1.1 for keyboard and mouse
RS-232 Reserved for hardware add-ons or high-level MS control by using
serial communication
P-Bus Reserved for instrument add-ons, using the internal EASY-nLC
instrument protocol bus:
8-wire control and limited power at 9/24 V
PS/2 Input for connection of keyboard or mouse
(discontinued
computer box only)
Monitor Output for connection of external display

1 Introduction
Specifications
Table 8. Hardware components

Item Specification
Pumps • 140 μL volume
(enough for a >10 h, 0–100% B, 300 nL/min gradient)
• 1 nL/min to 300 μL/min flow range
• External pressure sensor
Rotary valves • VICI™/Valco™ rotor/stator
• 6 ports
• 3 positions (1–6, 1–2, or CENTERED)
Autosampler • Peltier-cooled. Capacity is maximum 20 °C (68 °F) below
ambient temperature, measured at 60% RH. Expect less if
you remove the side panels, use an adapter plate in the
autosampler other than the standard plate, or both.
• Plate holder ejects through spring-mounted autosampler
door.
• 4 glass bottles with plastic lids for waste or wash liquids

2
Maintenance Schedule
To familiarize yourself with the maintenance schedule for the EASY-nLC instrument, review
this chapter.
Contents
• Daily Maintenance
• Weekly Maintenance
• Quarterly Maintenance
• Yearly Maintenance
• Field Service Repairs
Daily Maintenance
Check the solvent levels, draw fresh solvent through the solvent system, and flush air out of
the solvent system on a daily basis.
 To check the solvent levels
1. Visually inspect solvent bottle A, solvent bottle B, and the autosampler bottle in
position W3 (and the bottles in position W1 and W2 if used). Refill if necessary.
Tip You can also inspect the purity of the solvent to ensure no visible precipitates have
formed that might lead to blockages in the pump line.
2. Visually inspect the autosampler wash bottle in position W4 and the plastic waste beaker
in front of the solvent system compartment, and empty if necessary.
 To draw fresh solvent into the system and to flush air out of the system
Run the Purge Solvent scripts with two purge iterations, and run the Flush Air script
until flush volumes fall below 10 μL for the EASY-nLC II instrument or 12 μL for the
EASY-nLC 1000 instrument.

2Maintenance Schedule
Weekly Maintenance
Weekly Maintenance
Because the vapor pressures of formic acid, water, and acetonitrile differ, the solvent
composition changes over time. Refill the solvent bottles to maintain a consistent solvent
composition.
Quarterly Maintenance
Perform the following procedures quarterly (every 3 months).
 To check the back pressure
To test for system blockages, run the Back Pressure script for both solvents (see “Test –
Back Pressure” on page 48).
IMPORTANT The script evaluates the back pressure based on using 99.9% water for
solvent A and 99.9% acetonitrile for solvent B.
 To check the cooler temperature
Check that the actual plate temperature matches its set point (readout on the Home >
Overview page).
Figure 23. Cooler area of Autosampler dialog box
Set point Actual

temperature temperature
 To check the autosampler pickup function
Run the Sample Pickup script to check the sample pickup function (see “Test – Sample
Pickup” on page 42).
 To check the EASY-nLC solvent system for leaks
Run the Leaks script for “A+B” and for “System,” to check for and diagnose instrument
leaks. For more information, see “Test – Leaks” on page 44 and “Running a System Leak
Test” on page 218).
IMPORTANT Check the valve rotor shifts regularly. When the valve rotor shifts
exceed 6000, Thermo Fisher Scientific recommends checking the system for leaks.
From this point forward, perform leak tests every 1000 shifts and replace the rotor
seal when the leak test fails.

2 Maintenance Schedule
Yearly Maintenance
 To check the check valves
Run the Purge Solvent script (see “Prepare – Purge Solvent” on page 32) and do the
following:
• When the pumps are ejecting solvent, make sure that solvent is exiting the A and B
waste tubing into the waste beaker.
• When the pumps are refilling, make sure that no solvents are going into the pump
through the waste tubing.
If you detect a leaking check valve, replace it.
Yearly Maintenance
Replace the solvent filters and check the flow sensor calibration once a year.
 To exchange low-pressure solvent filters and high-pressure inline filters
Thoroughly clean new solvent filters before use as these can be a contamination source.
 To check the flow sensor calibration
Run the Flow Sensor calibration script with the Inspection Only parameter enabled (see
“Calibrate – Flow Sensors” on page 51).
This checks that the flow sensor calibration is working within specifications.
Field Service Repairs

If any of these instrument components is irreparably damaged, contact your local Thermo
Fisher Scientific field service engineer for repairs:
• Autosampler or autosampler cooler
• Rotary valve
• Pump (for both instruments) or pump PCB (for the EASY-nLC II instrument)
• Integrated computer
• Touch-screen monitor
CAUTION Chapter 5, “Field Service Maintenance,” describes how to replace these

instrument components. However, only a Thermo Fisher Scientific field service engineer
can perform these procedures. Attempted repairs by untrained personnel might cause
personal injury or irreparably damage the instrument.

3
Maintenance Scripts and Service Records

To familiarize yourself with the maintenance scripts and record keeping features provided by
the EASY-nLC software, review this chapter.
Contents
• Maintenance Scripts
• Keeping Service Records
• Checking and Resetting the Device Usage Counters
Maintenance Scripts
The EASY-nLC touch-screen software includes a variety of built-in maintenance scripts that
help you prepare the instrument for use and troubleshoot instrument problems.
 To select a maintenance script
1. On the touch screen, press Maintenance > Scripts.

2. Select a category and then the script for the specific operation you want.
You can also schedule some of the scripts for execution using the job queue.
Each of the following topics combines the category with the actual script name.
Prepare category Test category Calibrate category
• Prepare – Purge Solvent • Test – MS Connection • Calibrate – Valve Tune

• Prepare – Flush Air • Test – Sample Pickup • Calibrate – Flow Sensors
• Prepare – Precolumn Equilibration • Test – Leaks • Calibrate – Reset Pressure Sensor
• Prepare – Analytical Column Equilibration • Test – Valve Check • Calibrate – Direct Infusion
• Prepare – Isocratic Flow • Test – Back Pressure
• Test – Autosampler Torque
• Test – Pump Torque

3 Maintenance Scripts and Service Records
Maintenance Scripts
Prepare – Purge Solvent

The Purge Solvent script fills the selected pump or pumps with solvent and then ejects it into
the waste beaker. Use the Purge Solvent script when exchanging solvents, removing air from
the solvent lines, or filling the pumps.
Figure 24 shows the parameters for the Purge Solvent script.

Figure 24. Purge Solvent script parameters
 To run the Purge Solvent script
1. Open the Purge Solvent script as follows:

a. On the touch screen, press Maintenance > Scripts.
b. In the Category list, select Prepare.
c. In the Name list, select Purge Solvent.
2. Set up the parameters for this script as follows:
a. Press the Parameters tab.
b. In the Purge Iterations box, enter the number of empty/fill cycles to be performed:
• To refresh solvents on a daily basis, enter 2 iterations.
• To exchange solvents, enter a minimum of 10 iterations.
Note Entering a value of zero (0) for purge iterations refills the pump.
c. Select the check boxes for the appropriate pump or pumps.

3. Press Start.

Maintenance Scripts
Prepare – Flush Air

The Flush Air script removes air from inside the pump head by pressurizing the pump and
then releasing that pressure into the flow path toward the waste beaker.
The pump refills, pressurizes, releases pressure, and empties for each iteration of the script.
While the instrument executes the script, the software calculates the pressurization time
dynamically based on measurements from previous iterations and measures the pumped
volume required to reach 200 bar.
Note Because the solvents are slightly compressible and the pump itself expands, even an
air-free pump allows some pumping before reaching 200 bar.
Depending on the solvents, a pumped volume less than 10 μL for the PLF pump model
or 12 μL for the PLU pump model is acceptable.
Note Figure 8 on page 9 shows the PLF and PLU model pumps. While the PLU model
pump is standard in EASY-nLC 1000 instruments and the PLF model pump is standard
in most EASY-nLC II instruments, the PLU model pump is the replacement part for both
instrument models.
Figure 25 shows the parameters for the Flush Air script.

Figure 25. Flush Air script parameters

Maintenance Scripts
 To run the Flush Air script
1. Open the Flush Air script as follows:

a. Press Maintenance > Scripts.
c. In the Name list, select Flush Air.
b. In the Flush Threshold [μL] box, enter the acceptable threshold for the pump model:
• For the PLF pump (standard in most EASY-nLC II instruments), enter 10.
• For the PLU pump (standard in the EASY-nLC 1000 instrument), enter 12.
3. Press Start.
The script ends after the first iteration that gives a flush volume below the set threshold.
Prepare – Precolumn Equilibration

The Precolumn Equilibration script equilibrates the precolumn with solvent from pump A.
Use this script to equilibrate or flush the precolumn and to determine a suitable flow rate for
the sample loading step in your method.
Figure 26 shows the parameters for the Precolumn Equilibration script.

Figure 26. Precolumn Equilibration script parameters

Maintenance Scripts
 To run the Precolumn Equilibration script
1. Open the Precolumn Equilibration script as follows:

c. In the Name list, select Precolumn Equilibration.
b. Enter the appropriate values:
• In the Volume [μL] box, enter the volume of solvent A to use to equilibrate the
precolumn.
For best results, use at least 10 column volumes to equilibrate the precolumn.
• In the Flow [μL/min] box, enter the flow rate for the precolumn equilibration
step.
If the flow field is left empty, the pump operates at the set pressure.
• In the Max Pressure [bar] box, enter the maximum allowed pressure.
If the pressure field is left empty, the pump operates at the set flow (as long as it is
below the instrument maximum pressure of 300 bar for the EASY-nLC II
instrument or 1000 bar for the EASY-nLC 1000 instrument). If both a flow and
a max pressure are specified, the pump flow is limited by whichever parameter is
reached first.
CAUTION Check the maximum pressure rating for the precolumn. Running
the instrument at pressures higher than the column’s maximum pressure
rating reduces the column lifespan.
3. Press Start.

Maintenance Scripts
Prepare – Analytical Column Equilibration

The Analytical Column Equilibration script equilibrates the analytical column with solvent
from pump A.
Use this script to equilibrate or flush the analytical column, determine a suitable equilibration
flow rate for the method, or initialize a new analytical column.
Figure 27 shows the parameters for the Analytical Column Equilibration script.
Figure 27. Analytical Column Equilibration script parameters
Note The Analytical Column Equilibration script sets the valves to these positions:
• Valve A: 1–6
• Valve B: Center
• Valve S: 1–2
• Valve W: 1–2

Maintenance Scripts
 To run the Analytical Column Equilibration script
1. Open the Analytical Col Equilibration script as follows:

c. In the Name list, select Analytical Col Equilibration (abbreviated to fit in the space
allotted).
b. In the Volume [μL] box, enter the volume of solvent A to use to equilibrate the
analytical column.
For best results, use at least 10 column volumes to equilibrate the analytical column.
c. In the Flow box [μL/min], enter the flow rate for the analytical column equilibration
step.
If the flow field is left empty, the pump operates at the set pressure.
d. In the Max Pressure [bar] box, enter the maximum allowed pressure.
If the pressure field is left empty, the pump operates at the set flow (as long as it is
below the instrument maximum pressure of 300 bar for the EASY-nLC II instrument
or 1000 bar for the EASY-nLC 1000 instrument).
If both a flow and a maximum pressure are specified, the pump flow is limited by
whichever parameter is reached first.
CAUTION Check the maximum pressure rating for the analytical column.
Running the instrument at pressures higher than the maximum pressure rating
for the column reduces the column lifespan.
3. Press Start.

Maintenance Scripts
Prepare – Isocratic Flow

The Isocratic Flow script runs solvents A and B at a fixed mixture ratio. The script uses the
AFC system to accurately control the flow. Use this script to tune the mass spectrometer at a
given B percentage or when cleaning the instrument, the columns, or both. Figure 28 shows
the parameters for the Isocratic Flow script.
Figure 28. Isocratic Flow script parameters
 To run the Isocratic Flow script
1. Select the Isocratic Flow script as follows:

c. In the Name list, select Isocratic Flow.
2. Set up the parameters (see Figure 28) for this script as follows:
b. Enter the appropriate values:
• In the Volume box [μL], enter the total volume to be delivered by the pumps.
Note If you select the Run Indefinitely check box, the software ignores this
volume setting.
• In the Flow box [μL/min], enter the flow rate to be used.

• In the AB Mix box [%B], enter the solvent composition as a percentage of
solvent B.
• If you want the solvent flow to continue until you press Stop, select the Run
Indefinitely check box.

Maintenance Scripts
3. Press Start.
When either pump runs out of solvent, both pumps refill. The refilling process takes
approximately 2 minutes.
Test – MS Connection
The MS Connection script tests the contact closure function between the EASY-nLC
instrument and the mass spectrometer.
Figure 29 shows the MS connection script.
Figure 29. MS Connection script
 To run the MS Connection script and test the contact closure connection
1. Connect the contact closure cable to the EASY-nLC instrument and the mass
spectrometer.
Figure 30 shows the contact closure cable for an EASY-nLC instrument to be used with a
Thermo Scientific mass spectrometer.
Figure 30. Thermo Fisher contact closure cable

Maintenance Scripts
Tip Use the Thermo Fisher contact closure cable (LC160) to make contact closure
between the EASY-nLC instrument and a Thermo Scientific mass spectrometer.
Connect the two-pin connector to the mass spectrometer’s Start In pins. Connect the
12-pin connector to the back panel of the EASY-nLC instrument.
2. Check the contact closure settings for the LC/MS system as follows:
a. On the EASY-nLC touch screen, press Configuration > Connections.
b. For a Thermo Scientific mass spectrometer, make the following selections:
• In the Instrument (cable no.) list, select Thermo Scientific (LC160).
• In the Protocol list under Contact Closure Settings, select One-way.
• In the State at Start list under Contact Closure Settings, select Open.
3. Turn on the mass spectrometer and set it up to wait for a contact closure signal.
• For a third-party mass spectrometer, follow the instructions in the documentation
provided with the mass spectrometer. Then, go to step 5.
• For an LTQ Series mass spectrometer, go to step 4.
4. For an LTQ Series mass spectrometer, set up the mass spectrometer to wait for a contact
closure signal as follows:
a. Open the Tune Plus window.
b. On the menu bar, choose Control > Acquire Data.
Figure 31 shows the Control menu of the Tune Plus window for an LTQ Series mass
spectrometer.
Figure 31. Control menu
The Acquire Data dialog box opens (see Figure 32).

Maintenance Scripts
c. In the Start Mode area, select the Contact Closure option.

Figure 32. Acquire Data dialog box with the Contact Closure option selected
d. Click Start.
The mass spectrometer remains in the Waiting for Contact Closure state until it
receives a contact closure signal.
5. Send the contact closure signal from the EASY-nLC instrument to the MS detector as
follows:
a. On the EASY-nLC touch screen, press Maintenance > Scripts.
The Maintenance Scripts page opens.
b. In the Category list, select Test.
c. In the Name list, select MS Connection.
d. Press Start.
The EASY-nLC instrument sends a contact closure signal to the mass spectrometer.
The contact closure signal triggers the mass spectrometer to start scanning. The Scan
LED on the front panel of a Thermo Scientific mass spectrometer flashes blue when
the contact closure signal is set up correctly.

Maintenance Scripts
Test – Sample Pickup

The Sample Pickup script tests the accuracy of the autosampler pickup function. During the
script, the XYZ robotic arm moves to the specified sample location. Then pump S aspirates
the specified volume from the vial or microplate well and ejects this volume to waste. To
determine if the autosampler is aspirating the specified sample volume, weigh the sample both
before and after you run the test script as described in “Checking Sample Pickup” on
page 263.
Use this script to verify the calibration of the XYZ robotic arm and to determine the
appropriate flow rate (aspiration rate by pump S) setting in the method (or Xcalibur
instrument method) that you plan to use for your samples. The appropriate flow rate depends
on the sample viscosity.
Figure 33 shows the parameters for the Sample Pickup script and the Position dialog box that
opens when you press the value box for the Position parameter.
Figure 33. Sample Pickup script parameters

Maintenance Scripts
 To run the Sample Pickup script
1. Load the autosampler with the appropriate samples.
Tip For more information about running this script and testing the accuracy of the
sample pickup function, see “Checking Sample Pickup” on page 263.
2. Open the Sample Pickup script as follows:

c. In the Name list, select Sample Pickup.
b. In the Volume box [μL], enter the volume to be picked up.
c. In the Flow box [μL/min], enter the flow rate that pump S uses to aspirate the
sample. For aqueous samples enter 20 μL/min.
d. In the Position box, specify the position of the sample in the autosampler. See the
Position dialog box in Figure 33.
4. Press Start.

Maintenance Scripts
Test – Leaks
The Leaks script tests for possible leaks at the pump seal and in the flow path from the pump
to its associated valve (high-pressure subsystems A or B). The Leaks script can also test for
system leaks in the flow path downstream of valves A and B.
Use this script when you suspect leak problems in the pumps (pump piston seals), in the flow
path between the pump outlet and the associated valve, or downstream of valves A and B. For
information about running the system leak test, see “Running a System Leak Test” on
page 218.
Note You cannot perform the leak test for pump S, as it does not operate under pressure
during normal batch execution.
Figure 34 shows the parameters for the Leaks script

Figure 34. Leaks script parameters
During the leak test of pump A or B, the following events occur.
Step Event
1 The pump refills.
2 The associated valve centers, blocking the solvent flow through the valve.
3 The pump builds pressure to 280 bar for the EASY-nLC II instrument or 980 bar
for the EASY-nLC 1000 instrument.
4 When the pressure stabilizes at 280 bar for the EASY-nLC II instrument or 980 bar
for the EASY-nLC 1000 instrument, the pump calculates the flow loss based on the
pump piston movement required to maintain this pressure. If the flow loss is less
than 400 nL/min, the pump passes the leak test.

Maintenance Scripts
During a system leak test (Leaks script with System selected), the script pressurizes the flow
paths shown with red dashed lines in Figure 35, monitors the flow sensors and pump piston
movement, and identifies the location of a leak. Before you run a system leak test, you must
connect the Column Out line to the Waste In line with the HPLC union.
Figure 35. Pressurized lines for a system leak test
Pump S
Pressure
sensor
Autosampler needle
Pump A
Pressure
sensor
1
2 6
A
3 4 5
↓ Flow sensor
1
2 6
S
3 4 5
Mixing Tee
Pump B Column Out line
Pressure Waste In Line

sensor
Flow sensor ↓
1 1
2 6 2 6
B W
3 4 5 3 4 5
Centered

Maintenance Scripts
 To run the Leaks script
1. Open the Leaks script as follows:

c. In the Name list, select Leaks.
b. To select pump A or B, both pumps, or the entire system flow path for the leak test,
press the cell in the Value column and make your selection from the list:
• To test the solvent path from pump A to valve A (upstream of valve A), select A.
• To test the solvent path from pump B to valve B (upstream of valve B), select B.
• To test the solvent path from pump A to valve A and from pump B to valve B
(upstream of pumps A and B), select A + B.
• To test the solvent path downstream of valves A and B, select System. Figure 35
on page 45 shows the pressurized solvent path for the system leak test.
3. For a system leak test, connect the Column Out line to the Waste In line using the union
supplied in the accessory kit as shown in Figure 35 on page 45.
Instrument Part number of the stainless steel union

EASY-nLC II SC600
EASY-nLC 1000 SC900
For information about troubleshooting system leaks, see “Troubleshooting the Results of the
System Leak Test” on page 221 and “Troubleshooting a Pump that Fails the Leaks Script” on
page 216.

Maintenance Scripts
Test – Valve Check

The Valve Check script performs a self-test for the selected valves of an EASY-nLC II
instrument.
Use this script when valves begin to move slowly or cannot reach the required positions and
after exchanging valve parts (rotor or stator).
IMPORTANT This script is only valid for EASY-nLC II valves with a serial number less
than V-009999. Make sure to record any numbers that the script generates. If the
overshoot is greater than 6, contact your local Thermo Fisher Scientific field service
engineer.
Figure 36 shows the parameters for the Valve Check script.

Figure 36. Valve Check script parameters
 To run the Valve Check script
1. Select the Valve Check script as follows:

c. In the Name list, select Valve Check.
b. Select the check boxes for the valves that you want to test.
3. Press Start.

Maintenance Scripts
Test – Back Pressure

The Back Pressure script determines instrument back pressure for solvent A and B. The script
runs at a preset flow and measures the back pressure on the system.
IMPORTANT Before you perform the Back Pressure script, ensure that the solvent A
bottle contains water and the solvent B bottle contains acetonitrile. This test is not valid
for other solvents.
Use this script to test for a blockage in the solvent system. Before running the script, connect
the Column Out line to the Waste In line as shown in Figure 35 on page 45.
Figure 37 shows the parameters for the Back Pressure script.

Figure 37. Back Pressure script parameters
 To run the Back Pressure script
1. Open the Back Pressure script as follows:

c. In the Name list, select Back Pressure.
b. Test solvent A, solvent B, or both A and B by selecting the corresponding check box
or check boxes.
3. Press Start.

Maintenance Scripts
Test – Autosampler Torque

The Autosampler Torque script measures the torque required to move the XYZ robot on each
of its axes for the ASC autosampler.
IMPORTANT Do not run this script for the ASA autosampler. Contact your local
Thermo Fisher Scientific representative before running this script.
Figure 38 shows the Description page of the Autosampler Torque script.

Figure 38. Autosampler Torque script description

Maintenance Scripts
Test – Pump Torque

For the PLU pump in the EASY-nLC 1000 instrument, the Pump Torque script measures the
actuator’s ability to generate pressure at predefined torque levels.
IMPORTANT Do not use this script for the PLF pump in the EASY-nLC II instrument.
Contact your local Thermo Fisher Scientific representative before running this script.
Figure 39 shows the parameters for the Pump Torque script.

Figure 39. Pump Torque script parameters
Calibrate – Valve Tune

The Valve Tune script automatically retunes the selected valve in the EASY-nLC II
instrument.
IMPORTANT This script is only valid for an EASY-nLC II valve with a serial number
below V–009999. Contact your local Thermo Fisher Scientific representative before
running this script, as running this script incorrectly will compromise the performance of
the instrument.

Maintenance Scripts
Calibrate – Flow Sensors

The Flow Sensors script calibrates the flow sensors for pumps A and B.
Use this script to do the following:

• Periodically check the accuracy of the flow sensor calibration for your maintenance
records (select the Inspection Only check box).
• Calibrate the flow sensors when you change the type of solvent in solvent bottles A or B
(clear the Inspection Only check box).
This calibration does not require any additional plumbing.
IMPORTANT Because the flow sensor calibration requires a stable operating

temperature, ensure that the instrument’s side panels are installed and that the instrument
has been on for a minimum of one-half hour.
Figure 40 shows the parameters for the Flow Sensors script.

Figure 40. Flow Sensors script parameters
 To run the Flow Sensors script
1. Open the Flow Sensors script as follows:

b. In the Category list, select Calibrate.
c. In the Name list, select Flow Sensors.

Maintenance Scripts

b. Select the check boxes for the flow sensors (A, B, or both) that you want to either
inspect or calibrate and inspect.
Note To calibrate and inspect the flow sensors, this script performs a two-point
calibration as follows:
1. Calibrates the 0 μL/min point.
2. Inspects and evaluates this first calibration point.
3. Calibrates the 500 μL/min point.
4. Inspects and evaluates this second calibration point.
When you select the Inspection Only check box, the script does not apply the
new calibration. Selecting the Fast Inspection option instead of the Exact
Inspection option reduces the duration of the inspection and evaluation steps
from 16 minutes to 5 minutes, without reducing the accuracy of the calibration.
c. Do one of the following:

• To check the accuracy of the current calibration (only inspect the current
calibration), select the Inspection Only check box.
Note When you select the Inspection Only check box, the program does not
recalibrate the flow sensors.
• To calibrate and inspect the flow sensors (and apply the new calibration), clear
the Inspection Only check box.
d. Select the inspection duration as follows:
• When you want an estimate of the flow sensor accuracy, select the Inspection
Only check box and the Fast Inspection option.
• When you are recalibrating the flow sensors, clear the Inspection Only check box
and select the Exact Inspection option.
3. Press Start.
Calibrate – Reset Pressure Sensor

This script auto-zeroes the pressure sensor.
IMPORTANT Performing this script incorrectly will compromise the performance of the
instrument. Contact your local Thermo Fisher Scientific representative before running
this script.

Maintenance Scripts
Calibrate – Direct Infusion

Use the Direct Infusion script to analyze samples by direct infusion or to optimize the spray
stability by infusing a known peptide.
In a direct infusion experiment, sample is introduced into the mass spectrometer without
chromatographic separation by an analytical column. The EASY-nLC instrument picks up the
sample volume from the specified location, and then pumps it directly into the ion source
using the solvent flow from pump A.
Figure 41 shows the parameters for the Direct Infusion script.

Figure 41. Direct Infusion script
 To set up the system for a direct infusion experiment
1. Connect an emitter to the Column Out tubing.

Figure 42 shows an example of a direct infusion setup for an EASY-nLC 1000
instrument.
Figure 42. Setup for a direct infusion experiment
1/32 in. fitting Emitter and sleeve

Column Out line PEEK adapter union for 1/16 in. OD and 1/32 in. OD tubing
1/16 in. fitting
2. Mount the assembly onto your nanoflow ion source.

Maintenance Scripts
 To run the Direct Infusion script
1. Select the Direct Infusion script as follows:

b. In the Category list, select Calibrate.
c. In the Name list, select Direct Infusion.
b. In the Pickup Volume [μL] box, enter the volume that you want the autosampler
needle to pick up. The autosampler loads this volume into the sample loop.
c. In the Pickup Flow [μL/min] box, enter the flow rate at which pump S aspirates the
sample from the vial or well.
d. In the Pickup Position box, enter the vial or well position.
e. In Infusion Volume box [μL], enter the volume that pump A delivers to the system to
backflush the sample from the sample loop out through the Column Out line and
into the mass spectrometer’s ion source.
f. In the Infusion Flow [μL/min] box, enter the flow rate at which pump A moves the
sample into the mass spectrometer’s ion source.
g. Select the Wash check box to add a Wash step after pump A has pumped the specified
volume of solvent A through the system.
During the Wash step, pump S empties 100 μL of solvent A through the loop and
needle to the waste bottle.
3. Press Start.
IMPORTANT The Direct Infusion script flushes the solvent lines before it ends.
Stopping the script before it ends can leave sample solution in the flow path.
4. If you press Stop before the script ends, follow the instructions in message box that
appears to make sure that the current sample is flushed from the system (see Figure 43).
Figure 43. Wash instructions that appear when you stop the Direct Infusion script

Keeping Service Records
Keeping Service Records

Use the Maintenance > Log Book page to electronically enter all the service actions that you
perform on the instrument.
 To record a service action
1. Press Maintenance > Log Book.

The Maintenance > Log Book page opens (see Figure 44).
Figure 44. Log Book page of the Maintenance menu tab
2. Press Enter Log Entry.

The Log Entry dialog box opens.
3. In the box at the top of the dialog box, enter a description of the service action.
4. In the Templates list, select a template.
The Templates list contains the following selections: Comment, New Part, Maintenance,
Property Change, and Precolumn Changed by <User> on <Date>.
5. In the Components list, select a hardware component.
The Components list contains the following selections: None, Gradient, Valve B, Valve A,
Valve S, Valve W, Analytical Column, Precolumn, Autosampler, Pump A, Pump B, and
Pump S.

Checking and Resetting the Device Usage Counters
6. Do one of the following:

• Press Add to add this entry and keep the Log Entry dialog box open.
• Press Add and Close to add this entry and close the Log Entry dialog box.
• Press Close to close the Log Entry dialog box without saving any entries.
 To search the log
1. In the Log Book list, select Queue Job or User.

2. In the User List, select Any, Admin, or Guest.
3. In the Time From list, select a time.
4. In the Time To list, select a time.
5. Press Search.
The search results appear in the Search Result table.
Checking and Resetting the Device Usage Counters

The EASY-nLC system tracks the volume pumped by pumps A, B, and S and the number of
valve and rotor shifts for valves A, B, and S.
 To view the device usage values
1. Press Maintenance > Devices.

2. Do one the following:
• To view the volume pumped by a pump, select the pump from the list of devices.
• To view the number of valve and rotor shifts for a valve, select the valve from the list
of devices.
3. Press the Summary tab.
The Summary view opens.
 To reset the volume pumped or reset the rotor shifts to zero
1. Open the appropriate Summary page.

2. Press Reset.
For a pump, the value in the Intermediate Volume box resets to 0. For a valve, the value in
the Rotor Shifts box resets to 0.

4
Routine Maintenance
To maintain the EASY-nLC instrument, follow the maintenance procedures in this chapter.
Tip You can access most of the instrument components by removing either the left or
right side panel of the instrument. Three captive quarter-turn screws secure each panel to
the instrument housing.
• To remove a side panel from the housing, loosen (unlock) the screws from the housing
by rotating them 90° counterclockwise with a #2 Phillips head screwdriver. When
loosened, the screws rotate freely without constraint, but remain connected to the side
panel.
• To secure a side panel to the housing, mount the panel. Then tighten the screws to the
housing (lock) by rotating them 90° clockwise with a #2 Phillips head screwdriver.
For information about the suggested maintenance schedule and the built-in maintenance
scripts and record keeping features provided by the EASY-nLC software, see Chapter 3,
“Maintenance Scripts and Service Records.”
Contents
• Maintaining a Clean Working Environment
• Replacing the Main Power Fuse
• Maintaining the Syringe Pumps
• Maintaining the Rotary Valves
• Replacing the Check Valves
• Replacing an Inline Filter for the EASY-nLC 1000 Instrument
• Using nanoViper Fittings
• Replacing the Autosampler Needle
• Replacing the Sample Loop
• Replacing a Pressure Sensor for the PLU Pump
• Replacing a Flow Sensor
• Replacing the Hard Drive
• Managing the Devices List

4 Routine Maintenance
Maintaining a Clean Working Environment
Maintaining a Clean Working Environment

Maintain a clean working environment for the EASY-nLC instrument.
When cleaning the outside of the EASY-nLC instrument, use a mild detergent and a clean
cloth.
Replacing the Main Power Fuse

The EASY-nLC uses these fuses:
• For 120 Vac, the instrument uses one T 5 AL 250 V fuse (5 × 20 mm, IEC 60127).
• For 230 Vac, the instrument uses one T 2.5 AL 250 V fuse.
Use only UL Listed and CSA-certified fuses, All fuses supplied with the instrument are UL
Listed and CSA certified.
CAUTION Before removing the fuses, turn off the instrument and remove the power
cable.
 To replace the main power fuses
1. Move the EASY-nLC instrument to a benchtop where you can access the back panel.
Figure 45 shows the steps required to remove the fuse holder.
2. Turn off the power and pull out the power plug.
3. Place a flat-blade screwdriver into the slot in the top of the fuse holder, and then turn the
screwdriver to loosen the fuse holder.
4. Pull the fuse holder out of the power entry module.
Figure 45. Replacing the main power fuse
Turn off the power and pull the power plug Using a flat-blade screwdriver, loosen the
out of the power receptacle. fuse holder.

Replacing the Main Power Fuse
5. To install the appropriate fuse, do one of the following:

• Insert the 5 A fuse into the slot that aligns with the white triangle at the end of the
110–120 V line power text.
• Insert the 2.5 A fuse into the slot that aligns with the white triangle at the end of the
220–240 V text.
6. Make sure that the fuse ends align with the mounting brackets.
Note The fuse holder holds two fuses. One fuse is for a 220–240 V line power and
the other is for a 110–120 V line power.
7. Insert the fuse holder into the power entry module in the orientation that corresponds to
the operating power.
The triangle to the right of the voltage rating points toward the white mark at the bottom
of the power entry module (see Figure 46).
Figure 46. Power entry module
Appropriate orientation for

220–240 line voltage

Maintaining the Syringe Pumps

Each pump contains a piston seal and a piston. Over time, the buffered solutions leave
deposits on the pistons, and through constant contact with the moving pistons, the piston
seals slowly deteriorate.
Note Most EASY-nLC II instruments contain PLF model pumps, which have been
discontinued. If this pump is damaged, you must replace the PLF model pump with a
PLU model pump.
Both the EASY-nLC 1000 instrument and new shipments of the EASY-nLC II instrument
use PLU model pumps.
Figure 8 on page 9 shows the two pump models.
To replace a pump piston seal and clean the piston, follow these procedures:
1. “Retracting the Piston” on page 61
2. Depending on the pump model, follow one of these procedures:
• “Replacing the Piston Seal and Cleaning the Piston in a PLF Pump” on page 62
• “Replacing the Piston Seal in a PLU Pump” on page 67
3. “Priming the Pump” on page 71
4. “Resetting the Pump Usage Counter” on page 72
5. “Removing Air After Replacing a Piston Seal or a Pump” on page 73
6. Depending on whether you are performing maintenance on one of the chromatography
pumps (pump A or B) or on the sample pump (pump S), follow one of these procedures:
• For pumps A and B, run a pump leak test as described in “Running the Leaks Script
after Replacing a Piston Seal or a Pump” on page 73.
• For pump S, run a sample pickup test as described in “Test – Sample Pickup” on
page 42.

Retracting the Piston

Set the pump piston to the fully retracted position by running the Purge Solvent script with 0
iterations.
 To retract the pump piston
1. On the touch screen, press Maintenance > Scripts.

2. In the Category list, select Prepare.
3. In the Name list, select Purge Solvent.
4. Press the Parameters tab.
5. In the Purge Iterations box, enter 0 (see Figure 47).
Figure 47. Purge solvent script with 0 iterations
6. Select the check box for the appropriate pump.

7. Press Start.
The piston moves backward until it reaches the 140 μL position.
8. To replace the piston seal, go to the piston seal replacement procedure for your pump.
• “Replacing the Piston Seal and Cleaning the Piston in a PLF Pump” on page 62
–or–
• “Replacing the Piston Seal in a PLU Pump” on page 67

Replacing the Piston Seal and Cleaning the Piston in a PLF Pump
Most EASY-nLC II instruments have PLF model pumps (see Figure 8 on page 9).
Note To replace the piston seal in a PLU pump, follow the instructions in “Replacing the
Piston Seal in a PLU Pump” on page 67.
Replacing a piston seal in the PLF pump requires these tools and materials.
Tools Parts and materials

• #2 Phillips head screwdriver • Powder-free safety gloves
• 13 mm open-ended wrench • LC/MS-grade methanol
• 1/4 in. open-ended wrench • LC/MS-grade acetonitrile
• Pipette • Piston seal and piston seal tool, P/N LC210
CAUTION Wear powder-free gloves and safety glasses when handling parts of the LC system
that come into contact with solvents.
 To replace the piston seal in a PLF model pump
1. If you have not already done so, set the piston to its fully retracted position as described in
“Retracting the Piston” on page 61.
2. Set the corresponding valve to the Center position as described in “Using the Valve
Controls” on page 204.
3. Close down the EASY-nLC instrument and turn off the power (see “Closing Down the
EASY-nLC Instrument” on page 21).
4. Using a #2 Phillips head screwdriver, with a quarter-turn loosen the three captive screws
that secure the right side panel to the instrument housing. Then remove the panel.

5. Remove the tubing connected to the pump head as follows:

• If a PEEK fitting is connected to the pump head, use a 13 mm open-ended wrench,
to remove it (see Figure 48).
Figure 48. Removing a PEEK fitting from the externally threaded pump head for a PLF
model pump
PEEK fitting connected to an

externally threaded pump head
• If a stainless steel fitting is connected to the pump head, use a 1/4 in. open-ended
wrench to remove it.
Figure 49 shows a stainless steel fitting connected to an internally threaded pump
head.
Figure 49. Internally threaded pump head for a PLF model pump

connected to an
internally threaded pump head

6. Using a 13 mm open-ended wrench, remove the pump head (see Figure 50).
Figure 50. Removing the pump head
Pump head (PLF model pump)
7. Clean the piston as follows:

a. Place the piston in the fully extended position as follows:
i. Turn on the instrument and log in as an administrator.
ii. Press Home > Overview.
iii. Press the pump icon for the pump you want to control.
The Pump dialog box opens.
iv. In the flow rate box, enter the flow rate: 300 μL/min.
v. In the volume box, enter the dispense volume: 140 μL.
vi. Press Start.
b. Soak a lint-free tissue in methanol, and then squeeze out the excess solvent.
c. Clean the piston with the lint-free tissue soaked in methanol, and visually inspect the
piston for any scratches. Take care to avoid solvent drips, as the pump printed circuit
board can be damaged by exposure to solvents.
CAUTION The pump PCB is easily damaged by exposure to solvents.
d. Return the piston to the fully retracted position as follows:

i. In the Pump dialog box, set the flow rate to – 300 μL/min and the dispense
volume to 140 μL.
ii. Press Start.
8. When the piston is fully retracted, close down the EASY-nLC system and turn off the
power (see “Closing Down the EASY-nLC Instrument” on page 21).

9. Remove the worn piston seal as follows:

a. To avoid contaminating the pump head, clean the piston seal tool and guide tool by
soaking them in a beaker filled with 100% HPLC-grade methanol.
Figure 51 shows the piston seal tool.
Figure 51. Piston seal tool for the PLF model pump
Piston seal tool
Guide tool
b. Insert the piston seal tool into the worn piston seal and pull the piston seal out of the
pump head (Figure 52).
Figure 52. Using the piston seal tool to remove the worn piston seal (PLF model pump)
Worn piston seal
10. Install the new piston seal as follows:

a. Insert the guide tube into the pump head flange (see Figure 53).
Figure 53. Guide tool inserted into the pump head flange (PLF model pump)
Guide tool
b. Using a pipette, fill the groove in the piston seal with methanol.
Tip Filling the piston seal groove with methanol before installing the seal reduces
the time required for the Flush Air script to remove air from the pump.

c. Place the new seal with the groove facing upward on the piston seal tool
(see Figure 54).
Figure 54. Piston seal mounted onto the piston seal tool (PLF model pump)
d. Insert the piston seal tool into the guide tool (see Figure 55).
Figure 55. Inserting the piston seal tool into the guide (PLF model pump)
e. Push the piston seal tool into the guide until you feel resistance (see Figure 56).
Figure 56. Seating the piston seal (PLF model pump)

f. Remove the guide tube and the piston seal tool. and then check that the piston seal is
properly seated (see Figure 57).
Figure 57. Piston seal properly seated in the pump head (PLF model pump)
11. Using a 13 mm open-ended wrench, reconnect the pump head to the pump body.
12. Go to “Priming the Pump” on page 71.
Replacing the Piston Seal in a PLU Pump

Replacing the piston seal in a PLU model pump requires these tools and materials.

• 3 mm L-hex wrench • LC/MS-grade methanol
• 1/4 in. open-ended wrench • LC/MS-grade acetonitrile
• Pipette • Piston seal and piston seal tool, P/N LC510
 To replace the piston seal in a PLU model pump
1. If you have not already done so, set the piston to its fully retracted position as described in
“Retracting the Piston” on page 61.
3. Close down the EASY-nLC instrument and turn off the power (see “Closing Down the
EASY-nLC Instrument” on page 21).

5. Remove the used piston seal as follows:

a. Using a 1/4 in. open-ended wrench, remove the stainless steel fitting connected to the
pump head (see Figure 58).
Figure 58. Stainless steel fitting connected to the pump head (PLU model pump)
b. Using a 3 mm L-hex wrench, remove the two screws that secure the pump head to
the pump body (see Figure 59).
IMPORTANT Do not move the piston if the pump head has been removed.
Doing so can affect the piston alignment, which might cause the piston
calibration to be lost and result in irreversible piston damage.
Figure 59. Using a 3 mm L-hex wrench to remove the pump head

Two screws that secure
the pump head to the pump body
c. Clean the exposed portion of the piston with a lint-free tissue soaked in HPLC-grade
methanol and visually inspect the piston for scratches. Ensure that no solvent runs
into the pump.

d. Using only your fingernails or a plastic tool, remove the old seal from the pump head
(see Figure 60).
CAUTION Avoid using a metal tool to remove the piston seal from the pump
head, as metal can scratch the inside of the pump head and generate leaks.
Figure 60. Worn piston seal installed in the pump head (PLU model pump)
6. Install the new piston seal as follows:

a. With the spring side of the piston seal facing upward, mount the new piston seal onto
the piston seal tool (see Figure 61).
Figure 61. Piston seal mounted on the piston seal tool (PLU model pump)
Piston seal spring
b. Using a pipette, fill the rim of the piston seal with 100% LC/MS-grade methanol to
remove the air from the piston seal spring (see Figure 62).
Figure 62. Filling the piston seal with methanol (PLU model pump)

c. Place the pump head on the guide rods and evenly press it all the way down against
the piston seal tool to insert the seal into the pump head (see Figure 63).
Figure 63. Inserting the piston seal into the pump head (PLU model pump)
d. Gently pull the pump head off of the guide rods (see Figure 64).
Figure 64. Removing the pump head from the piston seal tool (PLU model pump)
7. Using the two screws and a 3 mm L-hex wrench, reconnect the pump head to the pump
body. Do not connect the stainless steel tubing to the pump head.
8. Go to the next procedure, “Priming the Pump.”

Priming the Pump

After you replace a piston seal, prime the pump with the appropriate solvent before you
reconnect the solvent line to the pump head.
 To prime the pump
1. Turn on the EASY-nLC instrument and log in as an administrator.

2. Set the piston to its fully extended position as follows:
a. On the touch screen, press Home > Overview.
b. Press the pump icon for the pump that you want to control.
The Pump X dialog box opens, where X identifies the pump (A, B, or S).
c. Set the flow rate to 300 μL/min and the volume to 140 μL.
d. Press Start.
3. Fill the pump head with solvent as follows:
a. Pipette an aliquot of the appropriate solvent into the pump head (see Figure 65).
Figure 65. Adding solvent to the pump head
CAUTION Be careful not to spill solvent on the PCBs.

• For the PLU pump model (standard in the EASY-nLC 1000 instrument and
replacement part for both EASY-nLC instruments), the LED panel cover for each
pump protects the PCB from accidental contact when the instrument’s right
panel is removed. However, the cover does not form a waterproof seal with the
pump body so that the PCBs are exposed to solvent leaks from above.
• For the PLF pump model (EASY-nLC II instrument), the printed circuit boards
are completely exposed.

b. In the Pump dialog box, set the flow rate to –300 μL/min and the volume to 140 μL.
Then press Start.
The piston moves down, drawing the solvent into the pump.
c. Make sure the pump head is filled with solvent during the entire retraction of the
piston.
4. Reconnect the solvent line to the pump head as follows:
• For a PLF pump with a PEEK fitting (see Figure 48 on page 63), use a 13 mm
open-ended wrench to tighten the fitting.
• For a PLF pump with a stainless steel fitting (see Figure 49 on page 63) or a
PLU pump, use a 1/4 in. open-ended wrench to tighten the fitting.
5. Mount the right side panel to the instrument housing. Then, with a #2 Phillips head
screwdriver, secure the panel by rotating the three captive screws a quarter-turn clockwise.
After you reconnect the pump head to the pump body and the high-pressure line from the
pressure sensor to the pump head, reset the pump usage counter, and then remove air from
the system.
Note You reset the usage counters before removing air from the system because the air
removal procedure requires the pump to go through 10 purge cycles.
Resetting the Pump Usage Counter

Reset the pump usage counter after you prime the pump.
 To reset the pump usage counter
1. On the touch screen, press Maintenance > Devices.

2. Select the pump from the list of devices.
3. Press the Summary tab.
4. Press Reset.
The value in the Intermediate Volume box resets to 0.
For more information, see “Checking and Resetting the Device Usage Counters” on
page 56.

Removing Air After Replacing a Piston Seal or a Pump

To draw fresh solvent through the solvent system and to remove air from the solvent system
components, including the pump heads, follow these procedures after you prime the pump
and reset the usage counters.
 To draw fresh solvent into the system and remove air from the system
1. To draw fresh solvent into the system and remove air from the solvent lines, do the
following:
c. In the Name list, select Purge Solvent (see “Prepare – Purge Solvent” on page 32).
d. Press the Parameters tab.
e. In the Purge Iterations box, enter 10.
f. Select the check box for the appropriate pump.
g. Press Start and wait for the system to perform 10 purge cycles.
2. To remove air from the pump head, do the following:
a. In the Name list, select Flush Air (see “Prepare – Flush Air” on page 33).
b. Press the Parameters tab.
c. Set the flush volume threshold to 10 μL for the PLF pump or 12 μL for the PLU
pump.
Note Figure 8 on page 9 shows the PLU and PLF pump models.
d. Press Start, and wait for the script to finish.
Running the Leaks Script after Replacing a Piston Seal or a Pump

After you prime pump A or pump B, reset the usage counters, remove air from the system,
and run a pump leak test.
Note For pump S, run a sample pickup test as described in “Test – Sample Pickup” on
page 42.
For information about replacing a pump, see “Replacing a Pump” on page 150. Only a
Thermo Fisher Scientific field service engineer can replace a damaged pump, as replacing the
pump is an advanced maintenance procedure.
 To run a pump leak test on a replacement pump or a pump with a new piston seal
Follow the instructions in “Test – Leaks” on page 44. When the instrument is leak tight,
the instrument is ready for use.

Maintaining the Rotary Valves

The EASY-nLC instrument has four rotary valves labeled Valve A, Valve B, Valve S, and
Valve W. These valves contain the same internal components.
To determine if the valve requires maintenance, run the Leak test script as follows:
• For valves S and W, run the Leaks script on the system (System).
• For valves A and B, run the Leaks script on the respective subsystem (A or B).
To maintain the valves, follow these procedures:

• “Cleaning the Rotor Seal and Stator,” on this page
• “Replacing the Rotor Seal” on page 77
• “Replacing the Stator” on page 78
Maintaining the valves by cleaning the rotor seal and stator or by replacing the rotor seal, the
stator, or both parts requires these tools and materials.
Tools Materials
• 9/64 in. hex wrench • Powder-free safety gloves
• 1/4 in. open-ended wrench • LC/MS-grade methanol
• #2 Phillips head screwdriver • Lint-free cloth
Cleaning the Rotor Seal and Stator

If a rotary valve is leaking, attempt to remove the leak by cleaning the rotor seal and the stator
before taking the more costly step of replacing the rotor seal.
To clean the rotor seal and stator in a valve and return the instrument to normal operation,
follow these steps:
1. “To remove the stator from the valve” on page 75
2. “To clean the rotor seal and the stator” on page 75
3. “To reassemble the cleaned valve and return the instrument to normal operation” on
page 76

 To remove the stator from the valve
1. Close down the EASY-nLC instrument, and then turn off the power to the instrument
(see “Closing Down the EASY-nLC Instrument” on page 21).
3. Using a 9/64 in. L-hex wrench, remove the two hex screws that secure the stator to the
valve assembly, and then pull the stator away from the valve driver.
4. Depending on whether you are cleaning or replacing the rotor seal, go to the appropriate
procedure:
• “To clean the rotor seal and the stator,” on this page
• “To replace the rotor seal” on page 77
Note If you are cleaning the valve components or replacing only the rotor seal, you do
not need to remove the tubing connected to the stator. If you are replacing the stator,
you must remove all the solvent lines from the valve.
 To clean the rotor seal and the stator
1. If you have not already done so, remove the stator from the valve as described in the
previous procedure, “To remove the stator from the valve.”
2. Leave the rotor seal mounted to the valve driver (see Figure 66). Clean the mounted rotor
seal with a lint-free tissue or Q-tip soaked in methanol.
Figure 66. Rotor seal mounted on the valve driver
Rotor seal
3. Clean the stator with a lint-free tissue or Q-tip soaked in methanol (see Figure 67).
Figure 67. Cleaning the stator

 To reassemble the cleaned valve and return the instrument to normal operation
1. Mount the clean stator onto the valve driver.

2. Using a 9/64 in. L-hex wrench, tighten the two hex screws a little at a time by shifting
from one screw to the other and back again until the screws are evenly torqued.
4. Turn on the EASY-nLC instrument and log in as an administrator or a super user.
5. Go to the next procedure, “To remove air from the system and check for leaks after
disassembling a valve.”
 To remove air from the system and check for leaks after disassembling a valve
1. If you removed the stator from valves A or B, flush air from the system as follows:
a. Set up the Flush Air script as described in “Prepare – Flush Air” on page 33.
b. Select the pump that is connected to the affected valve.
c. Set the flush volume threshold to 10 μL for the EASY-nLC II or 12 μL for the
EASY-nLC 1000.
d. Press Start.
e. Wait for the script to finish.
2. Check the system or subsystem for leaks as follows:
• If you removed the stator from in valve A or B, run the Leaks script for the affected
valve (see “Test – Leaks” on page 44).
• If you replaced the rotor seal in valve S or W, run the Leaks script for the system.
When the system is leak tight, the instrument is ready for use.

Replacing the Rotor Seal

If cleaning the rotor seal and stator does not remove the system leak, replace the rotor seal.
Replacing the rotor seal requires one of these parts.
Valve serial number Replacement part

V-010000 and above Rotor seal, P/N LC228
V-009999 Rotor seal, P/N LC224
Tip The About page of the Rotary Valve view on the Maintenance > Devices page lists the
serial number of the selected valve.
To replace the rotor seal in a valve and return the instrument to normal operation, follow
these steps:
1. “To remove the stator from the valve” on page 75
2. “To replace the rotor seal,” on this page
3. “To reset the usage counter for the valve” on page 78
4. “To remove air from the system and check for leaks after disassembling a valve” on
page 76
 To replace the rotor seal
1. If you have not already done so, access the rotor seal by following “To remove the stator
from the valve” on page 75.
2. Remove the rotor seal from the valve driver (see Figure 68).
Figure 68. Rotor seal mounted on the valve driver
Rotor seal
3. Carefully mount the new rotor onto the valve driver, ensuring that the rotor sealing
surface (engraved flow passage), is facing out.
4. If you have not already done so, clean the stator with a lint-free tissue or Q-tip soaked in
methanol.
5. Mount the clean stator onto the valve driver.

 To reset the usage counter for the valve
1. Turn on the EASY-nLC instrument and log in to the system as an administrator.

2. Reset the usage counter for the valve as follows:
a. Press Maintenance > Devices.
b. Select the valve from the list of devices.
c. Press the Summary tab.
d. Press Reset.
The value in the Rotor Shifts box resets to 0.
For more information, see “Checking and Resetting the Device Usage Counters” on
page 56.
3. To remove air from the system and check for leaks, follow “To remove air from the system
and check for leaks after disassembling a valve” on page 76.
Replacing the Stator

Replacing the stator requires one of these parts.
Valve serial number Replacement part

V-001000–V-099999 Coated stator, P/N LC226
V-000100–V-000999 Uncoated stator, P/N LC225
Tip The About page of the Rotary Valve view on the Maintenance > Devices page lists the
serial number of the selected valve.
To replace the stator in a valve and return the instrument to normal operation, follow these
steps:
1. “To remove the stator from the valve assembly” on page 79
2. “To install the new stator” on page 79
3. “To remove air from the system and check for leaks after disassembling a valve” on
page 76

 To remove the stator from the valve assembly
1. Close down the EASY-nLC system, and then turn off the power to the instrument
3. Disconnect the solvent lines from the valve as follows:
• Use a 1/4 in. open-ended wrench to remove stainless steel fittings.
• Use the black nanoViper knurled nut to loosen and remove nanoViper fittings.
4. Using a 9/64 in. L-hex wrench, remove the two hex screws that secure the stator to the
valve driver, and then pull the stator away from the valve driver.
 To install the new stator
1. Mount the new stator onto the valve driver.

3. Reconnect the solvent lines to the valve as follows:
• For stainless steel fittings, use a 1/4 in. open-ended wrench to tighten the fittings.
• For the nanoViper fittings in an EASY-nLC 1000 instrument, follow the instructions
in “Using nanoViper Fittings” on page 83 to reconnect the nanoViper solvent lines to
the valve ports. Take care not to overtighten these fingertight fittings.
4. To remove air from the system and check for leak, follow “To remove air from the system
and check for leaks after disassembling a valve” on page 76.

Replacing the Check Valves
Replacing the Check Valves

If a check valve is not functioning, replace it.
Replacing a check valve requires the following tools and materials.

• 9/16 in. open-ended wrench • Powder-free safety gloves
• #2 Phillips head screwdriver • Solvent-side check valve, P/N LC233
• Waste-side check valve, P/N LC234
 To replace a check valve
3. Do the following:
• For a solvent-side check valve, remove the solvent inlet line from the check valve, and
then terminate the solvent line with a plug.
• For a waste-side check valve, remove the waste line from the check valve.
CAUTION To prevent solvent from siphoning out of the solvent bottle on top of
the instrument and onto system components, use a plug to terminate a solvent
inlet line when you disconnect it from the solvent-side check valve.
The pump PCB is easily damaged by contact with solvents.

• For a solvent-side check valve, use a 9/16 in. open-ended wrench to loosen the valve
from the check valve assembly.
• For the waste-side check valve, remove the check valve by turning it counterclockwise
with your fingers.
5. Screw the new check valve onto the check valve assembly. Using a 9/16 in. open-ended
wrench, slightly tighten the solvent-side check valve to the assembly.

Replacing an Inline Filter for the EASY-nLC 1000 Instrument

• For a solvent-side check valve, reconnect the solvent inlet line.
• For a waste-side check valve, reconnect the waste line.
8. Run the Purge Solvent script for the pump associated with the replaced check valve, and
monitor the flow from the solvent bottle when the pump is filling and the flow to the
waste beaker when the pump is emptying (see “Prepare – Purge Solvent” on page 32).

Inline filters are connected to both the inlet and outlet ports of the flow sensors. The inline
filter consists of a stainless steel body (nut, filter, and tube) and a ferrule (see Figure 69).
Figure 69. Inline filter components (nut with integrated tube and filter and ferrule)
Replacing an inline filter requires the following tools and materials.

• #2 Phillips head screwdriver • Inline filter
 To install an inline filter into the receiving port of a flow sensor

3. While holding the wide end of the ferrule toward the nut, slide the ferrule over the tube
that extends from the threaded end of the nut.
IMPORTANT The inline filters have a swept volume (flow path volume) of less than
one microliter.
To prevent leaks, take care to properly seat the ferrule in the receiving port. Once the
ferrule is swaged onto the tubing, do not connect the fitting to a different receiving
port.
4. Using a 5/16 in. open-ended wrench, tighten the nut.

5. Install the nanoViper solvent inlet line into the inline filter (see Figure 70).
Figure 70. Installed inline filters
Inline filter
6. Run the Back Pressure script and the Leak script on the system as described in these
topics:
• “Test – Back Pressure” on page 48
• “Test – Leaks” on page 44

Using nanoViper Fittings
Using nanoViper Fittings

For the EASY-nLC instrument, most of the plumbing connections are made with nanoViper
fittings (see Figure 71).
Note For more information about working with nanoViper fittings, see “Using
nanoViper Fittings Quick Reference Guide” on page 323.
Figure 71. nanoViper fitting
Removable, black
PEEK sealing surface knurled tightening tool
Screw
Even though nanoViper fittings can withstand UHPLC backpressures of up to ~1034 bar
(~15 000 psi), they are fingertight fittings, which require only very small torques to seal.
Therefore, you must follow the guidelines below to avoid damage by overtightening.
 To use a nanoViper fitting
1. Insert the nanoViper fitting into the target port and slowly rotate the screw clockwise
until you feel resistance.
2. Using the black knurled tightening tool, turn the screw clockwise to an angle between
0 and 45 degrees (1/8-turn).
3. Run the Leaks script for the system as described in “Running a System Leak Test” on
page 218.
When the leak test ends, the system is at atmospheric pressure.
IMPORTANT To extend the lifetime of the nanoViper fittings, open and close
connections at atmospheric system pressures only. Opening and closing connections
at high system pressures can reduce the lifetime of the fitting system.
4. If the Leaks script fails because the new connection is not leak tight, use the black knurled
tightening tool to turn the screw by as much as an additional 45 degrees. Do not turn the
screw beyond an angle of 90 degrees from where you felt the initial resistance.
IMPORTANT To prevent damage to the sealing surface of the nanoViper fitting, take
care not to overtighten the nanoViper fitting.

Replacing the Autosampler Needle

Replacing the autosampler needle requires these tools and materials.

• #2 Phillips head screwdriver • ASA autosampler needle, P/N LC251
• ASC autosampler needle, P/N LC302
 To remove the autosampler needle from an ASC or an ASA model autosampler
2. Using a 1/4 in. open-ended wrench, unscrew the nut that secures the autosampler needle
to port 1 of valve S. Then remove the fitting from the port.
Figure 72 and Figure 73 show the solvent line connections to valve S for the
EASY-nLC II solvent system and the EASY-nLC 1000 solvent system, respectively.
Figure 72. Valve S solvent line connections for the EASY-nLC II instrument
Valve S
1
1
2 6
Autosampler
6
2
needle
3 5
5
3
4 From the
pressure sensor
Column Out
line From the
mixing Tee
Figure 73. Valve S solvent line connections for the EASY-nLC 1000 instrument
Valve S
1
Autosampler 2 6
needle
5
3 From the
pressure sensor
4
Column Out
From the
line
mixing Tee

3. Remove the nut, ferrule, and sleeve from the needle tubing.
Figure 74. Autosampler tubing with a nut, ferrule, and sleeve at one end
4. Depending on the instrument model, move the z-axis needle holder to an accessible
location within the tray compartment by doing the following:
• For the ASA model, go to step 5.
• For the ASC model, go to step 6.
5. For the ASA model, move the z-axis needle holder to position A1 as follows:
a. Press Home > Overview.
b. Press the Autosampler icon.
The Autosampler dialog box opens.
c. In the XYZ Robot area, select position A1 in the Well box (see Figure 75).
Figure 75. Autosampler direct control dialog box
d. Press Goto.
e. Go to step 7 on page 86.
6. For the ASC model, move the z-axis needle holder to position W1 as follows:
b. Press the Autosampler icon.

c. In the XYZ Robot area, press Go to Calibration.

The Tools page of the Autosampler view on the Maintenance > Devices page opens
(see Figure 76).
Figure 76. Tools page of the Autosampler view on the Maintenance > Devices page
d. In the Manipulator area, press Reset.

The z-axis needle holder moves to the W1 position.

8. Depending on the instrument model, do the following:

• For the ASC model, remove the black needle holder from the slot in the metal plate
that separates the solvent system hardware from the autosampler compartment.
Removing the fitting requires some gentle movement from both sides of the plate
(see Figure 77).
Figure 77. Removing the black needle holder from the slot in the metal plate
Black needle holder Slot in the

metal plate
• For the ASA model, remove the white plastic needle guide on the back of the
touch-screen monitor.
9. Loosen the nut that is connected to the z-axis needle holder by turning it
counterclockwise (see Figure 78). Then carefully pull the autosampler needle upward and
away from the holder.
Figure 78. Autosampler needle connected to the z-axis needle holder
ASA model z-axis needle holder ASC model z-axis needle holder

 To install a new autosampler needle
1. Mount the new autosampler needle in the z-axis holder. Check that the small spring is
situated between the PEEK nut and the plastic stop.
• For the ASC autosampler, go to step step 3.
• For the ASA autosampler, go to step step 4.
3. For the ASC autosampler, do the following:
a. Guide the end of the needle that connects to valve S through the large hole in the
metal plate that separates the tray compartment from the solvent system
compartment.
b. Install the black needle holder in the side plate.
4. For the ASA autosampler, slide the valve end of the tubing through the small plastic
holder on the back of the touch-screen monitor (see Figure 79).
Figure 79. Holder on the back of the touch-screen monitor
Holder
5. Connect the needle to port 1 of valve S as follows:

a. Slide the provided blue sleeve and metal fittings onto the tubing.
b. To ensure a zero dead volume connection, hold the blue sleeve and the tubing
firmly against the bottom of the valve port, and then tighten the fitting with a
1/4 in. open-ended wrench.
6. Recalibrate the needle position as described in Chapter 7, “Calibrating the Autosampler’s
XYZ Robot.”
7. Run 2 iterations of the Purge Solvent script for Pump S.
For information about running the Purge Solvent script, see “Prepare – Purge Solvent” on
page 32.
8. Run the Flush Air script for Pump S with a flush volume threshold of 10 μL for the
EASY-nLC II system or 12 μL for the EASY-nLC 1000 system.
For information about running the Flush Air script, see “Prepare – Flush Air” on page 33.

Replacing the Sample Loop
Replacing the Sample Loop

Thermo Fisher Scientific provides sample loops in several sizes for the EASY-nLC
instruments.
 To replace the sample loop
2. To remove the sample loop from the valve, do one of the following:
• For the EASY-nLC II instrument, use a 1/4 in. open-ended wrench to loosen the
fittings that secure the sample loop to ports 2 and 5 of valve S. Then remove the
sample loop from the valve.
Figure 80 shows the sample loop connections for the EASY-nLC II instrument.
Figure 80. Sample loop connections for the EASY-nLC II instrument
1
1
Sample loop 2
6
6
2
3 5
5
3
• For the EASY-nLC 1000 instrument, do the following:
a. Return the system to atmospheric pressure (see “Returning the System to

Atmospheric Pressure” on page 325).
b. Disconnect the nanoViper fittings connected to ports 2 and 5 of valve S.
Figure 81 shows the sample loop connections for the EASY-nLC 1000 instrument.
Figure 81. Sample loop connections for the EASY-nLC 1000 instrument
Sample loop 2
6
5
3

Replacing a Pressure Sensor for the PLU Pump
3. Connect the replacement sample loop to valve S as follows:

a. Insert the fittings at the end of the sample loop into ports 2 and 5 of valve S.
b. Depending on the instrument model, secure the connections as follows:
• For the EASY-nLC II instrument, use a 1/4 in. open-ended wrench to tighten the
fittings.
• For the EASY-nLC 1000 instrument, secure the fittings to their receiving ports as
described in “Using nanoViper Fittings” on page 83. Take care not to overtighten
these fingertight fittings.
4. Check for leaks by running the system leak test as described in “Checking the Sample
Loop Connections for a Leak” on page 222.

This topic describes how to replace a pressure sensor that is compatible with the PLU model
pump (standard in EASY-nLC 1000 instruments).
Note For information about replacing a pressure sensor for a PLF model pump (standard
in most EASY-nLC II instruments), see “Replacing a Pressure Sensor for a PLF Pump” on
page 117.
Replacing the pressure sensor that is connected through solvent line tubing to a PLU model
pump requires these tools and materials.

• 1/4 in. open-ended wrench • Pressure sensor, P/N LC502
• 2.5 mm L-hex wrench or ball driver
To replace a pressure sensor that is connected to a PLU pump, follow these steps:
1. “To remove a pressure sensor from the instrument” on page 91
2. “To install the new pressure sensor” on page 92

 To remove a pressure sensor from the instrument
4. Using a 1/4 in. open-ended wrench, disconnect the stainless steel tubing attached to the
inlet and outlet ports of the pressure sensor.
5. Using a 2.5 mm L-hex wrench or ball driver, remove the two screws that secure the
pressure sensor L bracket to the instrument panel.
6. While holding the pressure sensor, use a 2 mm L-hex wrench to remove the two screws
that secure the pressure sensor to the bracket.
7. Disconnect the pressure sensor cable from the pump.
Figure 82 shows the pressure sensor connections.
Figure 82. Pressure sensor connections
One of two screws that secure the

pressure sensor to the L bracket
Screws that secure Solvent line

the L-bracket to the connections
instrument panel
One of two screws that secure the

pressure sensor to the L bracket
Pressure sensor
cable

Replacing a Flow Sensor
 To install the new pressure sensor
1. Using a 2 mm L-hex wrench and the screws that you removed in step 6 on page 91,
secure the new pressure sensor to the bracket.
2. Using a 2.5 mm L-hex wrench or ball driver and the screws that you removed in step 5 on
page 91, reconnect the pressure sensor bracket to the interior right panel of the
instrument.
3. Reconnect the stainless steel solvent lines to the inlet and outlet ports of the pressure
sensor. Using a 1/4 in. open-ended wrench, tighten the fittings.
5. Reconnect the pressure sensor cable.
6. Run the Flush Air script as described in “Prepare – Flush Air” on page 33.

The procedure for replacing the flow sensor differs between the EASY-nLC 1000 system and
the EASY-nLC II system.
Depending on the instrument model, follow one of these procedures to replace a flow sensor:
• “Replacing a Flow Sensor in the EASY-nLC 1000 Instrument,” on this page
• “Replacing a Flow Sensor in the EASY-nLC II Instrument” on page 96
Replacing a Flow Sensor in the EASY-nLC 1000 Instrument

Replacing a flow sensor in the EASY-nLC 1000 system requires these tools and materials.

• 8 mm open-ended wrench • Flow sensor A/B, P/N LC540
• 2.5 mm hex wrench or ball driver

To replace a flow sensor in the EASY-nLC 1000 system, follow these steps:
1. “To remove an EASY-nLC 1000 flow sensor,” on this page
2. “To install an EASY-nLC 1000 flow sensor” on page 95
 To remove an EASY-nLC 1000 flow sensor
3. Remove the nanoViper tubing and from the inlet and outlet of the flow sensor.
Figure 83 shows the flow sensors mounted behind the bracket. The flow direction is
labeled on the bracket.
Figure 83. Flow sensors
nanoViper fitting
Inline filter
Inlet end
Outlet end
Inline filter
nanoViper fitting
4. Using an 8 mm open-ended wrench, remove the inline filters from both ends of the flow
sensor (see Figure 83).

5. Remove the black cable from the flow sensor (see Figure 84).
Figure 84. Removing the cable from the flow sensor
6. Using an 2.5 mm hex wrench, remove the two screws that secure the flow sensor to the
bracket (see Figure 85).
Figure 85. Removing the screws attaching the flow sensor to the bracket
Location of screws that

secure flow sensor A

7. Remove the flow sensor (see Figure 86).

Figure 86. Removing the flow sensor
 To install an EASY-nLC 1000 flow sensor
1. Insert the new flow sensor behind the bracket.

2. Insert the two screws (Figure 85 on page 94) that secure the flow sensor to the bracket,
and tighten the screws with a 2.5 mm hex wrench.
3. Connect the black cable to the flow sensor (see Figure 84 on page 94).
4. Reinstall the inline filters on both ends of the flow sensor (see Figure 83 on page 93).
Tighten the fittings with an 8 mm open-ended wrench.
5. Reconnect the nanoViper tubing to both ends of the flow sensor (see Figure 83 on
page 93).
6. Replace the right side panel.
7. Turn on the EASY-nLC 1000 system, and wait one hour for the flow sensor to reach the
correct operating temperature.
8. Calibrate the new flow sensor by using the Flow Sensors script (see “Calibrate – Flow
Sensors” on page 51).

Replacing a Flow Sensor in the EASY-nLC II Instrument

Replacing a flow sensor in the EASY-nLC II instrument requires these tools and materials.

• 2.5 mm hex wrench or ball • Flow sensor A type SLG1430-150, P/N LC240
driver • Flow sensor B type SLG1430-025, P/N LC241
To replace an EASY-nLC II flow sensor, follow these steps:

1. “To remove an EASY-nLC II flow sensor,” on this page
2. “To install an EASY-nLC II flow sensor” on page 99
 To remove an EASY-nLC II flow sensor
3. Using a 2.5 mm hex wrench, remove the two screws (see Figure 87) that secure the flow
sensor bracket to the instrument panel.

Figure 87. Removing the two screws that secure the flow sensor bracket to the panel
2.5 mm hex screw
4. Remove the solvent lines from both ends of the flow sensor (see Figure 88).
Figure 88. Removing the solvent lines
Outlet ends
Inlet ends

5. Loosen the metal ring and remove the cable connected to the flow sensor (see Figure 89).
Figure 89. Removing the cable to the flow sensor
Cable
connected to
the flow sensor
6. Using a 2.5 mm hex wrench, remove the two screws that secure the flow sensor to the
bracket (see Figure 90).
Figure 90. Removing the screws that secure the flow sensor to the bracket
Two screws per

flow sensor

 To install an EASY-nLC II flow sensor
1. Install the new flow sensor into the bracket as follows:

a. Align the new flow sensor with the mounting holes in the bracket.
IMPORTANT You must replace flow sensor A with type SLG1430-150 and
flow sensor B with type SLG1430-025.
b. Insert the two screws that you removed earlier in step 6 of

“To remove an EASY-nLC II flow sensor,” into the bracket (see Figure 90 on
page 98).
c. Using a 2.5 mm L-hex wrench, tighten the two screws to secure the flow sensor to the
bracket.
2. Reconnect the cable to the flow sensor, and tighten the metal ring (see Figure 89 on
page 98).
3. Reconnect the solvent lines to both ends of the flow sensor (see Figure 88 on page 97).
4. Remount the bracket to the panel as follows:
a. Align the bracket with the mounting holes in the panel.
b. Insert the screws that you removed from the bracket when you removed it from the
panel.
c. Using a 2.5 mm L-hex wrench, tighten the two screws to secure the flow sensor
bracket to the panel (see Figure 87 on page 97).
6. Turn on the EASY-nLC II instrument.
7. Wait 30 minutes for the flow sensors to reach the proper operating temperature.
8. Calibrate the new flow sensor by using the Flow Sensors script (see “Calibrate – Flow
Sensors” on page 51).

Replacing the Hard Drive

Use this procedure to replace the hard drive in either the EASY-nLC 1000 instrument or the
Thermo Fisher Scientific supplies several versions of the hard drive. Order the appropriate
hard drive based on both the instrument model and the computer box where you are
replacing the hard drive. The discontinued versions of the computer box have a PS/2 port
(see Figure 91).
Figure 91. Comparison of computer ports between the obsolete and current computer boxes
Obsolete computer box Current computer box
PS/2 LAN MONITOR USB LAN RS-232 MONITOR
PS/2 port on the

back panel of the
obsolete computer box
Replacing the hard drive requires these tools and materials.
Tools Replacement part

2.5 mm hex wrench Hard drive:
Torx T-10 wrench • EASY-nLC II instrument:
 Compatible with obsolete computer box: P/N LC281
 Compatible with current computer box: P/N LC286
–or–
• EASY-nLC 1000 instrument:
 Compatible with obsolete computer box: P/N LC581
 Compatible with current computer box: P/N LC586
To replace the hard drive, follow these steps:

1. “To remove the hard drive” on page 101
2. “To install the hard drive” on page 103

 To remove the hard drive
1. Close down the EASY-nLC instrument, and then turn off the power to the instrument
2. Using a 2.5 mm hex wrench, loosen the two screws in the hard-drive drawer
(see Figure 92).
Figure 92. Screws that secure the hard-drive drawer (obsolete computer box shown)
Two screws that secure the hard-drive drawer
3. Pull out the hard-drive drawer, as shown in Figure 93.

Figure 93. Pulling out the hard-drive drawer

4. Using a Torx T-10 wrench, remove the four screws underneath the hard-drive drawer that
secure the hard drive to the drawer (see Figure 94).
Figure 94. Removing the screws underneath the hard-drive drawer
5. Unplug the hard drive from the IDE cable (see Figure 95).
Figure 95. Hard drive unplugged from the IDE cable
IDE cable
The flat (IDE) cable is connected to the hard disk. The text on the hard disk is upside
down, and the pins on the hard drive fit in the same place on the flat cable connector.

Tip If the IDE cable plug is difficult to access, remove the brass rod that holds the
cable down (see Figure 96). Use a Torx T-8 wrench to remove the screws. Place the
rod back in the drawer afterward.
Figure 96. Removing the brass rod that holds the cable down
 To install the hard drive
1. Insert the new hard drive.

2. Connect the hard drive to the IDE cable.
3. Insert the four screws into the holes underneath the hard-drive drawer and then, using a
Torx T-10 wrench, tighten the four screws to secure the hard drive to the drawer (see
Figure 94 on page 102).
4. Close the hard-drive drawer.
5. Using a 2.5 mm L-hex wrench, insert and tighten the two screws that secure the drawer to
the back panel (see Figure 92 on page 101).
6. Turn on the EASY-nLC instrument.
7. Press Vendor.
8. When prompted, enter the serial numbers for the instrument and the hard drive.

Note When you replace the hard drive, the pumps and valves are automatically
detected during the boot procedure. Because the autosampler is not detected by the
boot procedure, you must add it to the Device list. After you add the autosampler to
the Device list, you must calibrate the plate formats that you plan to use and the wash
bottle positions, as these calibrations were stored on the old hard drive.
9. Add the autosampler to the Devices list as follows:

b. Press Add Device.
The Select a Device to Add dialog box opens.
c. Locate the autosampler device and select it.
d. Press Accept to add the autosampler device to the Devices list and close the Select a
Device to Add dialog box.
e. Verify that the autosampler device was added to the system by locating it in the
Devices list.
10. Calibrate the autosampler as described in Chapter 7, “Calibrating the Autosampler’s XYZ
Robot.”

Managing the Devices List

The Device list on the Maintenance >Devices page lists the current devices installed in the
EASY-nLC instrument.
When you add or remove a device that is not automatically detected during the boot
procedure, you must add the device to or remove the device from the Devices list on the
Maintenance > Devices page. Devices that are not recognized during the boot procedure
include the autosampler and the external RePlay device.
 To add a device to the Device list

2. Press Add Device.
The Select a Device to Add dialog box opens.
3. Locate the device in the list and select it.

4. Press Accept to add the autosampler device to the Devices list and close the Select a
Device to Add dialog box.
5. Verify that the device was added to the system by locating it in the Devices list. Select the
device in the Devices list, and review the information on the About page.
 To remove a device from the Devices list

2. Select the device in the Devices list.
3. Press Remove Device.
The Remove Device dialog box appears.
4. Press Accept to remove the device and return to the Maintenance > Devices page.

 To view information about a device

2. Select the device in the Devices list.
3. Press the About tab.
The About view contains information about the serial numbers and firmware versions for
the rotary valves, piston (syringe) pumps, autosampler, and HPLC.

5
Field Service Maintenance

This chapter provides procedures for use by Thermo Fisher Scientific field service engineers
on replacing the subassemblies in the EASY-nLC instrument. Only Thermo Fisher Scientific
field service engineers can perform these procedures.
CAUTION Only Thermo Fisher Scientific field service engineers can perform the
procedures in this chapter.
Contents
• Replacing the Built-In Computer
• Replacing the Monitor
• Replacing a Pressure Sensor for a PLF Pump
• Replacing the ASC Autosampler
• Upgrading from an ASA Autosampler to an ASC Autosampler
• Replacing the Autosampler Cooler
• Replacing a Rotary Valve
• Replacing a Pump
• Replacing a Pump PCB

5 Field Service Maintenance
Replacing the Built-In Computer

The procedure for replacing the built-in computer is the same for the EASY-nLC 1000 and
EASY-nLC II instruments, except where noted.
Replacing the computer box requires the following part and tools.
Tools Parts
• #2 Phillips screwdriver Computer box:
• Torx T-10 wrench • EASY-nLC II instrument: P/N LC285
• Small flathead screwdriver
–or–
• EASY-nLC 1000 instrument: P/N LC585
To replace the built-in computer, follow these steps:

1. “To remove the computer box,” on this page
2. “To install the new computer box” on page 112
 To remove the computer box
1. Close down the EASY-nLC instrument (see “Closing Down the EASY-nLC Instrument”
on page 21), and then unplug the power cable.
2. Disconnect all of the cables from the instrument’s back panel.
that secure the left side panel to the instrument housing. Then remove the panel.
4. Remove the internal cables connected to the computer box.
Note The cable connectors can be hard to loosen. You might need to wiggle the
connectors carefully from side to side to loosen them.
Note Take care when you disconnect the monitor LVDS cable because it is easily
damaged.

Figure 97 shows these cables in the EASY-nLC 1000 instrument and Figure 98 shows
these cables in the EASY-nLC II instrument.
Figure 97. Cables connected to the computer box in the EASY-nLC 1000 instrument
LVDS cable
Figure 98. Cables connected to the computer box in the EASY-nLC II instrument
LVDS cable
Tip To remove the 12 V cables on the EASY-nLC II instrument, press the tab on the
top of the plug, as shown in Figure 99.
Figure 99. Pressing the tab on the top of the plug of the 12 V cables

5. Using a Torx T-10 wrench, remove the screws that secure the back panel to the
instrument (see Figure 100).
Note In older EASY-nLC instruments, 11 screws secured the back panel to the
housing. In current EASY-nLC 1000 instruments, 3 screws secure the back panel to
the housing.
Figure 100. Screws that secure the back panel to the instrument housing
P-BUS
HARD
DRIVE
I
O
110-120V▼
120/230 V : 50/60 Hz: 250 W

Fuse at 120 V– : T5 AL 250 V
Fuse at 230 V– : T2.5 AL 250 V
Made in U.S.A.
E A S Y- n L C 1 0 0 0
LC-011xxx
S/N
P/N
LC120
This device complies with Part 15 of the FCC Rules.

(1) This device may not cause harmful interference, and
(2) This device must accept any interference received, including interference
that may cause undesired operation.

6. Using a Torx T-10 wrench, remove the four screws that secure the computer box to the
Figure 101. Screws to remove from the computer box
7. Pull the computer box out of the EASY-nLC housing, as shown in Figure 102.
Figure 102. Pulling out the computer box

 To install the new computer box
1. Insert the new computer box into the EASY-nLC housing.

2. Reconnect all of the internal cables to the computer box.
• Figure 97 on page 109 shows the connections to the computer box inside the
• Figure 98 on page 109 shows the connections to the computer box inside the
3. Using a Torx T-10 wrench and the four screws that you removed in step 6 on page 111,
secure the computer box to the instrument (see Figure 101 on page 111).
4. Using a Torx T-10 wrench and the screws that you removed in step 5 on page 110, secure
the back panel to the instrument.
Tip Do not reconnect the left side panel to the instrument housing until after you
recalibrate the autosampler.
5. Reconnect the cables to the back panel as follows:

• Reconnect the power cable to the back panel and to a laboratory power outlet.
• If the instrument was connected to a laboratory LAN port, reconnect the Ethernet
cable.
• If the instrument is part of a Thermo Scientific LC/MS system, reconnect the
Ethernet cable to the back panel of the instrument, and make sure that the other end
of the cable connects to the Ethernet switch for the data system hardware.
6. Turn on the EASY-nLC instrument, and log in as an administrator.
7. Add the autosampler to the Devices list (see “Managing the Devices List” on page 105).
8. Recalibrate the autosampler (see Chapter 7).

Replacing the Monitor

The procedure for replacing the monitor is the same for the EASY-nLC 1000 instrument and
the EASY-nLC II instrument, except where noted.
Replacing the monitor requires the following part and tools.
Tools Part
• Torx T-10 wrench Monitor (and adapter cable for computer
boxes with a PS/2 keyboard connector as
• 2 mm L-hex wrench or straight wrench
shown in Figure 16 on page 16),
P/N LC282
To replace the monitor, follow these steps:

1. “To remove the monitor,” on this page
2. “To install the new monitor” on page 116
 To remove the monitor
on page 21), and unplug the power cable.
• For the EASY-nLC II instrument, go to step 3 to remove the front panel.
• For the EASY-nLC 1000 instrument, go to step 4 to remove the top-front panel.
3. To remove the front panel from the EASY-nLC II instrument, do the following:
a. Using a flat-edged tool, pry off the Thermo blue applique.
b. Using a Torx T-10 wrench, remove the 10 screws that secure the front plate to the
EASY-nLC II instrument. Then remove the plate (see Figure 103).
c. Go to step 5.
Figure 103. Removing the front plate from the EASY-nLC II instrument

4. To remove the top-front panel from the EASY-nLC 1000 instrument, do the following:
a. Using a Torx T-10 wrench, remove the two screws that secure the top-front panel to
the top back of the instrument.
b. Open the tray compartment door, and then use a Torx T-10 wrench to remove the
screw that secures the top-front panel to the front of the instrument.
5. Using a 2 mm hex wrench, remove the four screws that secure the monitor to the
CAUTION Use only hand tools with a hex tip to avoid damaging the screw heads.
Figure 104. Removing the screws from the front of the monitor
7. Remove the USB, LVDS, and monitor cables connected to the computer box, being
careful not to damage the LVDS plug (see Figure 105).
Figure 105. USB, LVDS, and monitor cables
USB cable
LVDS cable
Monitor cable

8. If a white plastic needle guide is installed on the back of the monitor, remove it before
removing the monitor.
Figure 106 shows the white plastic needle guide on the back of the monitor.
Figure 106. White plastic needle guide
Needle guide
9. Carefully remove the monitor by pulling it straight forward (see Figure 107).
Figure 107. Removing the monitor

 To install the new monitor
1. Carefully insert the new monitor into the instrument housing.

2. If you removed the white plastic needle guide on the back of the monitor, reinstall it.
Figure 106 on page 115 shows the white plastic needle guide mounted to the back of the
monitor.
3. If the computer box has a PS/2 keyboard connector on its back panel as shown in
Figure 16 on page 16, connect the adapter cable that is supplied with the new monitor to
the monitor cable.
4. Connect the USB, LVDS, and monitor cables to the computer box, being careful not to
damage the LVDS plug (see Figure 105 on page 114).
5. Using a 2 mm ball driver and the screws that you removed in step 5 on page 114, secure
the monitor to the instrument.
• For the EASY-nLC II instrument, use a Torx T-10 wrench and the 10 screws that you
removed in step b on page 113 to secure the front plate to the housing.
• For the EASY-nLC 1000 instrument, use a Torx T-10 wrench and the three screws
that you removed in step 4 on page 114 to secure the top-front panel to the housing.
7. Mount the left side panel to the instrument housing. Then, with a #2 screwdriver, secure
the panel by rotating the three captive screws a quarter-turn clockwise.
8. Plug in the power cable, and then turn on the EASY-nLC instrument.

Replacing a Pressure Sensor for a PLF Pump

The procedure for replacing a pressure sensor differs between EASY-nLC 1000 instruments
with PLU pumps and EASY-nLC II instruments with PLF pumps.
Note Most EASY-nLC II instruments contain the PLF pump model.
The following procedure explains how to replace a pressure sensor that is connected to a PLF
pump. For instructions about replacing a pressure sensor that is connected to a PLU pump,
see “Replacing a Pressure Sensor for the PLU Pump” on page 90.
Replacing the pressure sensor that is connected to a PLF pump requires these items.

• # 2 Phillips screwdriver • Powder-free gloves
• 2.0 mm L-hex wrench • Pressure sensor, P/N LC202
• 2.5 mm L-hex wrench or ball driver
• 1/4 in. open-ended wrench
To replace a pressure sensor that is connected to a PLF pump, follow these steps:
1. “To remove a pressure sensor that is connected to a PLF pump,” on this page
2. “To install a pressure sensor for a PLF pump” on page 121
 To remove a pressure sensor that is connected to a PLF pump
2. Close down the EASY-nLC II instrument (see “Closing Down the EASY-nLC
Instrument” on page 21), and unplug the power cable.

4. Disconnect the P-Bus communication cables from the pump (see Figure 108).
Figure 108. P-Bus communication cables connected to the pump PCB of the PLF pump
P-Bus communication cables
5. Using a 2.5 mm L-hex wrench or ball driver, remove the four 2.5 mm hex screws that
secure the PCB to the pump.
Figure 109 shows these screws. The lower right screw also connects the pressure sensor
grounding cable to the PCB.
Figure 109. Four hex screws connecting the PCB to the PLF pump
Pressure sensor
grounding cable

6. Gently pull the PCB toward you and rotate it to gain access to its back side
(see Figure 110).
Figure 110. Turning the PCB around (PLF pump)
Pressure sensor
communication cable
connection to the
back side of the PCB
7. Disconnect the pressure sensor communication cable, being careful not to put any stress
on the cables (see Figure 111).
Figure 111. Disconnecting the pressure sensor communication cable (PLF pump)
Pressure sensor
communication cable
connection to the
back side of the PCB

8. While holding the pressure sensor, use a 1/4 in. open-ended wrench to disconnect the
solvent lines connected to the inlet and outlet of the pressure sensor (see Figure 112).
Figure 112. Disconnecting the solvent lines from the pressure sensor
Solvent lines connected

to the pressure sensor
9. Using a 2.5 mm L-hex wrench or ball driver, remove the two hex screws that secure the
pressure sensor L bracket to the instrument panel (see Figure 113).
Figure 113. Pressure sensor L-bracket screws
Screws that secure

the pressure sensor
to the L bracket
Screws that secure
the L bracket to the
instrument panel
10. Using a 2 mm L-hex wrench or ball driver, unscrew the two hex screws that secure the
pressure sensor to the L-bracket (see Figure 113).

 To install a pressure sensor for a PLF pump
1. Disconnect and remove the pressure sensor from the EASY-nLC II instrument as
described in “To remove a pressure sensor that is connected to a PLF pump” on page 117.
2. Using a 2 mm L-hex wrench or ball driver, insert and tighten the two hex screws to secure
the pressure sensor to the L-bracket.
3. Using a 2.5 mm L-hex wrench or ball driver, insert and tighten the two hex screws
to secure the pressure sensor L-bracket to the instrument panel (see Figure 113 on
page 120).
4. Reconnect the solvent lines to the pressure sensor (see Figure 112 on page 120).
5. Reconnect the pressure sensor communication cable, being careful not to put any stress
on the cables (see Figure 111 on page 119).
6. Gently slide in the PCB.
7. Using a 2.5 mm L-hex wrench or ball driver, insert and tighten the four 2.5 mm
hex screws to connect the PCB to the pump (see Figure 109 on page 118).
Note The screw in the lower right also connects the pressure sensor grounding cable
to the PCB.
8. Reconnect the P-Bus communication cables to the pump (see Figure 108 on page 118).
9. Mount the right side panel to the instrument housing. Then, with a #2 screwdriver,
secure the panel by rotating the three captive screws a quarter-turn clockwise.
10. Turn on the EASY-nLC II instrument and log in as an administrator (see “Logging In to
the EASY-nLC Instrument for Maintenance Tasks” on page 20).
11. To draw fresh solvent into the pump, purge the pump five times by using the Purge
Solvent script on the Maintenance > Scripts page (see “Prepare – Purge Solvent” on
page 32).
12. To remove air from the system, run the Flush Air script for the pump associated with the
new pressure sensor (see “Prepare – Flush Air” on page 33).

Replacing the ASC Autosampler

The procedure for replacing the ASC autosampler is the same for the EASY-nLC 1000
instrument and the EASY-nLC II instrument. However, if your EASY-nLC instrument has an
installed ASA autosampler that is irreversibly damaged, you must upgrade to an ASC
autosampler, because the ASA autosampler is no longer available. For instructions on
upgrading to an ASC autosampler, see “Upgrading from an ASA Autosampler to an ASC
Autosampler” on page 128.
Replacing the ASC autosampler requires these items.

• #2 Phillips screwdriver • Powder-free gloves
• 3 mm L-hex wrench or ball driver • 4 in. or 10 cm length tie wrap
• Torx T-10 wrench • Autosampler (ASC), P/N LC301
• Cutting pliers
To replace the autosampler, follow these steps:

1. “To remove the ASC autosampler,” on this page
2. “To install the ACS autosampler into an instrument that previously included this model”
on page 127
 To remove the ASC autosampler
1. Remove the old autosampler from the device list as follows:

b. Select the autosampler in the Devices list.
c. Press Remove Device.
The Remove Device dialog box opens.
d. Press Accept.
on page 21). Then unplug the power cable.
2. Using a #2 Phillips head screwdriver, with a quarter-turn loosen the three captive
quarter-turn screws that secure each side panel to the instrument housing. Then remove
both panels.

3. Remove the computer box from the instrument as described in “To remove the computer
box” on page 108.
4. Unscrew the autosampler needle fitting, and remove or pull up the autosampler needle
from the needle holder.
Figure 114 shows the autosampler needle connected to the needle holder.
Figure 114. Needle connected to the needle holder
Autosampler needle
fitting
5. Unplug the bus cables on the left side of the instrument from the autosampler cooler and
horizontal XYZ-axis PCB (see Figure 115).
Figure 115. Bus cables
Cooler bus cable
XYZ-axis PCB bus

cable

6. Cut the tie wrap attaching the cables to the vertical part of the autosampler frame, as
shown in Figure 116.
Figure 116. Cutting the strip attaching the cables to the autosampler frame
7. Using a Torx T-10 screwdriver, remove the screws that secure the back horizontal cable
bar to the autosampler frame (see Figure 117).
Figure 117. Horizontal cable bar after removal of screws
Bus cable
connected to
valve B
Back left screw that secures the Autosampler

autosampler to the instrument frame
Horizontal cable bar

5Field Service Maintenance
8. Move the cable bar to the side (this is easier to do if you also remove the bus cable to
valve B). See Figure 118.
Figure 118. Horizontal cable bar moved aside
Valve B
Bus cable
disconnected from
valve B
Horizontal
cable bar
Back side of the Right side of the

autosampler autosampler
9. Using a 3 mm hex wrench, remove the three screws that secure the autosampler to the
bottom plate of the housing (see Figure 119, Figure 120, and Figure 121):
• Remove the screw from the right side of the autosampler (see Figure 119).
Figure 119. Removing the screw from the right side of the autosampler

• Remove the screw from the back left side of the autosampler (see Figure 120).
Figure 120. Removing the screw from the back left of the autosampler
• Remove the screw the screw on the front of the autosampler (see Figure 121).
Figure 121. Removing the front screw from the autosampler
10. Remove the autosampler from the housing through the back of the instrument.
Figure 122 shows the housing with the autosampler partially removed.
Figure 122. Housing with autosampler partially removed

 To install the ACS autosampler into an instrument that previously included this model
1. Insert the new autosampler into the housing.

2. Using a 3 mm L-hex wrench and, if necessary, a needle-nosed pliers or tweezers, insert
and tighten the screws that secure the autosampler to the bottom of the housing as
follows:
• Insert and tighten the screw on the back left side of the autosampler
(see Figure 120 on page 126).
• Insert and tighten the screw on the right side of the autosampler
• Insert and tighten the screw on the front of the autosampler
3. Insert and tighten the screws that secure the back horizontal cable bar to the autosampler
frame (see Figure 117 on page 124).
4. Install a new tie wrap to secure the cables to the vertical part of the autosampler frame.
5. Plug the bus cables into the autosampler cooler and horizontal XYZ-axis PCBs.
6. Reinstall the computer box as described in “To install the new computer box” on
page 112.
7. Reinsert the autosampler needle into the holder and tighten the fitting.
Tip Reconnect the left side panel to the housing after you recalibrate the autosampler.
9. Reconnect the power cable.

11. Add the ASC autosampler to the Devices list on the Maintenance > Devices page as
follows:
a. Press Maintenance > Devices to open the Maintenance > Devices page.
b. Press Add Devices to open the Select the Device to Add dialog box.
c. Select the ASC autosampler from the list, and then press Accept.
d. Verify that the ASC autosampler has been added to the Devices list.
i. Select the ASC autosampler in the Devices list.
ii. Check the information on the About page.
For more information about adding devices to the Devices list, see “Managing the
Devices List” on page 105.
12. Calibrate the autosampler as described in Chapter 7.

Upgrading from an ASA Autosampler to an ASC Autosampler

If your EASY-nLC II instrument has an ASA autosampler that is irreversibly damaged, you
must upgrade to an ASC autosampler because the ASA autosampler is no longer available.
Upgrading the instrument by replacing an ASA autosampler with an ASC autosampler

requires these items.

• 4 mm ballpoint hex wrench • Powder-free gloves
• 2 mm L-hex wrench or ball driver • M5 ×16 MC hex screw
• 2.5 mm L-hex wrench or ball driver • ASC autosampler, P/N LC301
• Torx T-10 wrench
• #2 Phillips screwdriver
• Tweezers
To replace the ASA autosampler with an ASC autosampler, follow these steps:
1. “To remove the ASA autosampler from the EASY-nLC II instrument,” on this page
2. “To install the ASC autosampler into an instrument that previously held the ASA model”
on page 130
 To remove the ASA autosampler from the EASY-nLC II instrument
1. Upgrade the touch-screen software to the latest version as described in “Downloading the
Latest Firmware File” on page 296.
Note Read the release notes before you upgrade to ensure that you have the most
recent version of the HPLC software.
2. Press Maintenance > Devices and remove the old autosampler from the device list.
on page 21). Then unplug the power cable.
4. Remove the computer box as described in “To remove the computer box” on page 108.
Note Removing the computer box requires the removal of the left side panel and the
back panel.

6. Remove the monitor as described in “To remove the monitor” on page 113.
7. Using a 2.5 L-hex wrench or ball driver, loosen valve W (see Figure 123).
Figure 123. Loosened valve W
Valve W
8. Disconnect the two P-Bus communication cables from the cooler PCB and
XYZ-axis PCB on the right side of the instrument (see Figure 129 on page 132).
9. Remove the ASA autosampler through the side of the housing.
10. Disconnect the cables that supply power to the fans, and remove the fan assembly at the
back of the housing (see Figure 124).
Figure 124. Removing the fan assembly and cables

 To install the ASC autosampler into an instrument that previously held the ASA model
Note Because you are upgrading the instrument by adding an ASC autosampler, this
upgrade procedure differs from the simple installation procedure on page 127.
1. As you insert the new autosampler into the housing, move the loosened valve W a little to
create the required space, as shown in Figure 125.
Figure 125. Putting in the ASC autosampler
2. Align the holes in the autosampler plate with the three mounting holes in the bottom of
the housing (see Figure 126).
Figure 126. Aligning the holes in the autosampler plate with the mounting holes

3. Reinstall the computer box into the EASY-nLC housing.

4. Reconnect all of the internal cables to the computer box.
Figure 98 on page 109 shows the connections to the computer box inside the
5. Insert the P-Bus terminator between the computer box and the P-Bus communication
cables as shown in Figure 127. It does not matter which cable the terminator connects to.
Note Do not install the connector if the computer box is labeled “Terminated,” as
shown in Figure 128. This designation means that you do not have to install a
separate terminator cable.
Figure 127. P-Bus connector inserted between the computer box and the P-Bus communication
cables
P-Bus connector
Figure 128. Computer box with “Terminated” label
“Terminated” label

6. Using a Torx T-10 wrench and the four screws that you removed in step 6 on page 111,
secure the computer box to the instrument (see Figure 101 on page 111).
7. Connect the P-Bus communication cables to the autosampler.
The longer cable connects to the cooler PCB. The shorter cable connects to the
XYZ-axis PCB. Figure 129 shows these two cables.
Figure 129. P-Bus communication cables
Figure 130 shows the boards that the P-Bus communication cables connect to.
Figure 130. Boards that the P-Bus communication cables connect to
Cooler PCB
XYZ-axis PCB
8. Using a 2.5 mm hex wrench or ball driver, mount valve W.

9. Secure the autosampler to the housing as follows:

a. Using a pair of tweezers, place the M5 × 16 hex screw in the back right mounting
position, lifting up the autosampler in order to put the screw in place.
Figure 131, Figure 132, and Figure 133 demonstrate this procedure.
Figure 131. Lifting up the autosampler to position the screw
Figure 132. Placing the M5 × 16 hex screw into the back right side of the autosampler
frame
Figure 133. The M5 × 16 hex screw in place

b. Insert the screw into the back left side of the autosampler. Use a ball driver to tighten
the screw (see Figure 134).
Figure 134. Securing the back left screw
c. Insert the screw into the front of the autosampler. Use a ball driver to tighten the
screw (see Figure 135).
Figure 135. Securing the front screw

10. Place the air filter from the ASA autosampler onto the ASC cooler (see Figure 136).
Figure 136. Placing the air filter onto the cooler
Because the injection needles are different for the ASA and ASC autosamplers, you must
install a needle arm that can be held in place underneath the mixing Tee holder.
11. Mount the aluminum needle arm under the mixing Tee holder (see Figure 137).
Figure 137. Aluminum needle arm
Mixing Tee holder
Needle arm
12. Place the mixing Tee in the holder. Use the aluminum needle arm when you attach the
needle (see Figure 138).
Figure 138. Needle
Mixing Tee
Needle arm Mixing Tee holder
13. Reinstall the monitor as described in “To install the new monitor” on page 116.
Tip Do not reconnect the left side panel to the instrument housing until after you
recalibrate the autosampler.
14. Turn on the instrument, and then log in to the instrument as an administrator.

15. Add the ASC autosampler to the Devices list on the Maintenance > Devices page as
follows:
The Maintenance > Devices page opens.
b. Press Add Devices.
The Select the Device to Add dialog box opens.
c. Select the ASC autosampler from the list, and then press Accept.
d. Verify that the ASC autosampler has been added to the Devices list.
For more information about adding devices to the Devices list, see “Managing the
Devices List” on page 105.
16. Calibrate the autosampler as described in Chapter 7, “Calibrating the Autosampler’s XYZ
Robot.”

Replacing the Autosampler Cooler

The procedure for replacing the autosampler cooler is the same for the EASY-nLC 1000 and
EASY-nLC II instruments, but it differs between an ASC cooler and an ASA cooler.
To replace the autosampler cooler, follow the appropriate procedure:

• “Replacing the ASC Cooler,” on this page
• “Replacing the ASA Cooler” on page 140
Replacing the ASC Cooler

Replacing the ASC cooler requires these items.
Tools Parts
• Torx T-10 wrench ASC autosampler cooling module, P/N LC310
• 2.5 mm L-hex wrench
To replace the ASC cooler, follow these steps:

1. “To remove the ASC cooler,” on this page
2. “To install the new ASC cooler” on page 139
 To remove the ASC cooler
1. Close down and turn off the EASY-nLC instrument (see “Closing Down the EASY-nLC
Instrument” on page 21). Then disconnect the power cable.
2. Using a Torx T-10 wrench, remove the screws on the back cover panel, and remove the
panel.
3. Access the PCB on the back of the cooler through the back of the instrument, and unplug
the P-Bus communication cables, shown in Figure 139.
Figure 139. P-Bus communication cables
P-Bus
communication
cables

4. Using a 2.5 mm ball driver, remove the two 2.5 mm hex screws at the bottom of the
cooler, shown in Figure 140.
Figure 140. Screws at the bottom of the cooler
5. Using a 2.5 mm ball driver, remove the 2.5 mm hex screw in the top center position of
the cooler, as shown in Figure 141.
The screws do not fall out when loosened, because they are held in place by O-rings.
Figure 141. Removing the top center screw

6. Pull out the cooler, as shown in Figure 142.

Figure 142. Pulling out the cooler
 To install the new ASC cooler
1. Insert the new cooler.

Be careful not to damage any of the cables during reassembly. Figure 143 shows a
damaged cable.
Figure 143. Damaged cable
Damaged cable
2. Using a 2.5 mm ball driver, insert and tighten the 2.5 mm hex screw in the top center
position (see Figure 151 on page 143).
3. Using a 2.5 mm ball driver, insert and tighten the two 2.5 mm hex screws at the bottom
of the cooler (see Figure 150 on page 143).
4. Plug the P-Bus communication cables into the PCB on the back of the cooler, accessing
the PCB through the back of the instrument.
5. Align the back panel to the back of the instrument.
6. Using a Torx T-10 wrench, tighten the eleven screws that secure the back panel to the
instrument.

Replacing the ASA Cooler

Replacing the ASA cooler in an EASY-nLC II instrument requires these items.
Tools Parts
• 2 mm L-hex wrench or ball driver ASA autosampler cooling module,
• 2.5 mm L-hex wrench or ball driver P/N EXLC252
• 3 mm L-hex wrench
• 5.5 mm open-ended wrench
• #2 Phillips screwdriver
To replace the ASA cooler, follow these steps:

1. “To remove the ASA cooler,” on this page
2. “To install the ASA cooler” on page 145
 To remove the ASA cooler
1. Close down and turn off the EASY-nLC instrument (see “Closing Down the EASY-nLC
Instrument” on page 21). Then disconnect the power cable.
2. Remove the autosampler door, shown in Figure 144, to avoid damaging it when you
remove the hex screws underneath the adapter plate holder.
Figure 144. Autosampler door

3. Depending on the instrument model, do one of the following:

• On the EASY-nLC II model LC100, use a 5.5 mm open-ended wrench to loosen the
nuts underneath the door (see Figure 145).
CAUTION Be careful removing the lid because the spring on the door can snap
back.
Figure 145. Nuts beneath the lid of the EASY-nLC II instrument
• On the EASY-nLC II model LC100-2, use a 2 mm L-hex wrench to loosen the screws
on the front (see Figure 146).
Figure 146. Screws on the front of the EASY-nLC II instrument (model LC100-2)

5. Using a flathead screwdriver or your fingernail, loosen the cap that secures the ribbon
cable to the controller PCB, as shown in Figure 147.
Figure 147. Loosening the ribbon cap on the controller PCB
Figure 148 shows a close-up view of the cap that secures the cable to the PCB.
Figure 148. Cap around the ribbon cable (close-up view)
6. Pull the ribbon cable out of the cap, as shown in Figure 149.
Figure 149. Pulling the ribbon out of the cap

7. Using a 2.5 mm L- hex wrench, remove the lid where the ribbon cable connects to the
autosampler tray (see Figure 150).
Figure 150. Removing the lid
8. Using a 2 mm hex wrench, remove the screws in the small PCB underneath the lid.
Figure 151 shows the screw in the lower right corner, and Figure 152 shows the screw in
the middle of the left side.
Figure 151. Loosening the screw in the lower right corner
Figure 152. Loosening the screw in the middle left side

9. Using a 3 mm L-hex wrench, loosen the four hex screws underneath the adapter plate
holder, and remove the holder. Figure 153 shows the location of these screws.
Figure 153. Screws beneath the adapter plate holder
10. Lift and pull the adapter plate holder out of the autosampler, as shown in Figure 154.
Figure 154. Pulling the adapter plate holder out of the autosampler
Note The sleeves around the holes on the bottom of the adapter plate holder can fall
out. Figure 155 shows these sleeves.
Figure 155. Hole sleeves on the bottom of the adapter plate holder
Sleeve that has

fallen out of the hole

 To install the ASA cooler
1. Align the arms of the autosampler bed, as shown in Figure 156.

Figure 156. Aligning the arms of the autosampler bed
2. Carefully place the new cooler in the autosampler bed, as shown in Figure 157.
Figure 157. Placing the new cooler in the autosampler bed
3. Verify that the cables from the fan are routed in the groove (see Figure 158).
Figure 158. Verifying the placement of the fan cables

4. Using a 3 mm L-hex wrench, insert and tighten the four hex screws underneath the
adapter plate holder. Figure 153 on page 144 shows the location of these screws.
5. Using a 2 mm L-hex wrench, tighten the two screws in the small PCB. Figure 151 on
page 143 and Figure 152 on page 143 show the locations of these screws.
6. Using a 2.5 mm L-hex wrench, mount the lid where the ribbon cable connects to the
autosampler cooler (see Figure 150 on page 143).
7. Insert the ribbon cable into the controller board (see Figure 147 on page 142 and
Figure 149 on page 142).
8. Using a flat screwdriver or your fingernail, push the cap around the ribbon cable in place
9. Reattach the autosampler door (see Figure 144 on page 140).
10. Verify that the autosampler moves smoothly in and out by moving it manually.
12. Turn on the EASY-nLC II instrument, and check the cooler temperature from the
Home > Overview page.
13. Before using the instrument, install the vial/plate adapter and perform an autosampler
calibration. For instructions, see Chapter 7, “Calibrating the Autosampler’s XYZ Robot.”

Replacing a Rotary Valve

The procedure for replacing a rotary valve is the same for the EASY-nLC 1000 instrument
and the EASY-nLC II instrument.
Replacing a high-pressure valve requires these items.

• 1/4 in. open-ended wrench • Switching valve:
• Torx T-10 wrench – EASY-nLC 1000 instrument: P/N LC519
• 2.5 mm L-hex wrench –or–
• Flathead screwdriver – EASY-nLC II instrument: P/N LC218
To replace a rotary valve, follow these steps:

1. “To remove a rotary valve,” on the page
2. “To install a new rotary valve” on page 149
 To remove a rotary valve
on page 21), and then unplug the power cable.
2. Remove the computer box as described in “To remove the computer box” on page 108.
Note Removing the computer box requires the removal of the left side panel and the
back panel.
4. From the right side of the instrument (solvent system compartment), remove the tubing
from the stator on the valve that you are replacing. Be careful to avoid pulling any fused
silica lines, as there is limited space around the valves.
Tip When replumbing the system, follow the solvent system schematics in
Appendix C, “Consumables and Replacement Parts.”

5. Using a 2.5 mm L-hex wrench, remove the four 2.5 mm hex screws that keep the valve in
place inside this compartment.
As you remove the last hex screw, the valve might slip down into the autosampler
compartment.
6. From the back of the instrument, disconnect the cables shown in Figure 159 from the
valve to be exchanged.
Figure 159. Cables connected to valves
7. Pull out the valve, as shown in Figure 160.

Figure 160. Pulling out a valve
Note If there is a support collar between the body of the valve and the body of the
EASY-nLC instrument, move it to the new valve.

 To install a new rotary valve
1. Using a small flathead screwdriver, set the rotary switch on the new valve of the PCB,
shown in Figure 161, to the same address as the valve being replaced:
• Valve A=1
• Valve B=2
• Valve S=3
• Valve W=4
Figure 161. Valve rotary switch
Rotary switch
2. Insert the new valve, making sure that the valve PCB faces down.
3. In the back of the instrument, connect the cables shown in Figure 159 on page 148 to the
new valve.
4. Using a 2.5 mm L-hex wrench, insert and tighten the four hex screws that keep the valve
in place inside the autosampler compartment.
5. In the solvent system compartment, restore the tubing and connections to the stator on
the valve that was replaced.
6. Reinstall the computer box as described in step 1 through step 5 of “To install the new
computer box” on page 112.
7. Mount the left and right side panels to the instrument housing. Then, with a #2
screwdriver, secure each panel by rotating the three captive screws a quarter-turn
clockwise.
8. Run the Flush Air script as described in “To run the Flush Air script” on page 34:
• Enter 12 μL for a PLU pump (standard in the EASY-nLC 1000 instrument).
• Enter 10 μL for a PLF pump (standard in most EASY-nLC II instruments).
9. Run the Leaks script for the subsystem that you have worked on as described in “To run
the Leaks script” on page 46.
• For valve A, select A.
• For valve B, select B.
• For valves W or S, select System.

Replacing a Pump
Replacing a Pump
The procedure for replacing a pump differs between EASY-nLC 1000 instruments that
contain PLU model pumps and EASY-nLC II instruments that contain PLF model pumps.
Note Because Thermo Fisher Scientific no longer stocks the PLF model pump as a
replacement part, you must replace both pump models with the PLU model pump.
To replace a pump, follow the appropriate procedure:

• “Replacing a PLU Pump,” on this page
• “Replacing a PLF Pump with a PLU Pump” on page 154
Replacing a PLU Pump

Replacing a PLU model pump requires these tools and materials.

• 1/4 in. open-ended wrench • PLU model pump, P/N LC501
• 2.5 mm hex wrench
• 3 mm hex wrench
• Pipette for priming the pump
To replace a pump in the EASY-nLC instrument, follow these steps:

1. “To remove a PLU model pump from an EASY-nLC instrument” on page 151
2. “To install a PLU pump in an EASY-nLC instrument” on page 153

Replacing a Pump
 To remove a PLU model pump from an EASY-nLC instrument
1. Set the valve for the pump to position 1–6 as follows:

b. Press the appropriate valve icon.
c. In the Valve dialog box, press Center.
Placing the valve in the Center position shuts off the solvent flow to the subsystem.
2. Close down and then turn off the EASY-nLC instrument.
3. Disconnect the power cable from the instrument’s back panel.
5. Using a 1/4 in. open-ended wrench, disconnect the stainless steel tubing connected to the
pump head, shown in Figure 162.
Figure 162. Fitting on the pump head
Fitting on
the pump
head

Replacing a Pump

• For the EASY-nLC 1000 instrument, unplug the flow sensor cable (from pump A
or B), the pressure sensor cable, and the P-Bus communication cables, shown in
Figure 163.
Figure 163. Flow sensor cable, pressure sensor cable, and P-Bus communication cables for
an EASY-nLC 1000 instrument
One of
four screws that One of four screws that
secure the pump secure the pump
to the panel to the panel
Flow sensor cable

Rotary switch
One of four screws that

secure the pump
One of to the panel
four screws that
secure the pump
Pressure
to the panel
sensor cable
P-Bus
communication
cables
• For the EASY-nLC II instrument, unplug the pressure sensor cable and the
P-Bus communication cables from the pump.
The EASY-nLC II flow sensors do not have a flow sensor cable that connects to the
pump.
7. Using a 3 mm ball driver or L-hex wrench, remove the four 3 mm hex screws that secure
the pump to the instrument panel, and then remove the pump. Set the screws aside.

Replacing a Pump
 To install a PLU pump in an EASY-nLC instrument
1. Connect the new pump as follows:

a. Using a 3 mm ball driver or L-hex wrench and the four 3 mm hex screws that you
removed in step 7 on page 152, secure the new pump to the instrument panel.
b. Depending on the instrument model, do one of the following:
• For the EASY-nLC 1000 instrument, reconnect the flow sensor cable, the
pressure sensor cable, and the P-bus communication cables.
• For the EASY-nLC II instrument, reconnect the pressure sensor cable and the
P-bus communication cables.
2. Make sure that the address setting on the pump PCB is the same as the setting for the old
PCB. Use a small flathead screwdriver to change the rotary switch address on the new
pump PCB.
• Pump A =1
• Pump B = 2
• Pump S = 3
3. Reconnect the power cable to the instrument’s back panel.

4. Turn on the EASY-nLC instrument, and log in as an administrator.
5. Prime the pump as described in “Priming the Pump” on page 71.
6. Reconnect the tubing to the pump head. Using a 1/4 in. open-ended wrench, tighten the
fitting.
7. Draw fresh solvent into the solvent lines and remove air from the pump head as described
in “Removing Air After Replacing a Piston Seal or a Pump” on page 73.
8. Depending on the pump you are replacing, do the following:
• When replacing pump A or B, run the pump leak test, and then run the flow sensor
calibration (see “Test – Leaks” on page 44 and “Calibrate – Flow Sensors” on
page 51).
• When replacing pump S, run the sample pickup test (see “Test – Sample Pickup” on
page 42).

Replacing a Pump
Replacing a PLF Pump with a PLU Pump

You must replace an irreparably damaged PLF pump in an EASY-nLC II instrument with a
PLU pump, as Thermo Fisher Scientific no longer stocks the PLF pump as a
replacement part.
When you replace a PLF pump with a PLU pump, do the following:
• Replace the pressure sensor for the pump and the high-pressure tubing associated with the
pump, as the PLU pump is not compatible with the pressure sensor used in the
• Upgrade the touch-screen software to version 3.1.4 or later, as the EASY-nLC II
instrument only supports the PLU pump when running software version 3.1.4 or later.
• If you are replacing pump S in an EASY-nLC II instrument with an earlier version of
the chassis, order and install the components in the Pump Mounting Kit so that the
PLU pump can fit into the pump S position.
Replacing an EASY-nLC II pump (PLF model) with a PLU pump requires these items.

• 1/4 in. open-ended wrench • Pipette
• 2 mm hex wrench or • PLU pump, P/N LC501

ball driver • Pressure sensor, P/N LC502
• 2.5 mm hex wrench or • Tubing between the pump and the pressure sensor:
ball driver – Pumps A and S: PEEK tubing, P/N LC212
• 13 mm open-ended wrench – Pump B: prebent stainless steel tube, P/N LC215
• Small flathead screwdriver • Tubing between the pressure sensor and the rotary
valve:
• 3 mm open-ended wrench
– Pumps A and S: PEEK tubing, P/N LC213
– Pump B: prebent stainless steel tube, P/N LC216
 To replace a PLF pump with a PLU pump in the EASY-nLC II instrument
1. Upgrade the touch-screen software to version 3.1 or later.

If the touch-screen software is older than version 2.7.8, you must first upgrade to
version 2.7.8, and then upgrade to version 3.1.
For information about upgrading the software, refer to Appendix B of the EASY-nLC
Series Getting Started Guide (for the touch-screen software). You can find the touch-screen
software files in the user zone on www.proxeon.com.

Replacing a Pump
2. Before you remove the right side panel, do the following:

a. Set the corresponding valve to the Center position as described in “Using the Valve
b. Close down the EASY-nLC II instrument, and then turn off the power switch on the
instrument’s back panel (see “Closing Down the EASY-nLC Instrument” on
page 21).
c. Disconnect the power cable from the instrument’s back panel.
Figure 164 shows the solvent line connections from pump A to valve A, which are made
with PEEK tubing. The solvent line connections from pump B to valve B are made with
stainless steel tubing.
Figure 164. Pump connections in an EASY-nLC II instrument (PEEK tubing for pump A)
Valve A Valve A
1 1
6
6
2
2
5
5
3
3
4 4
0 1
9
2 3
7 8
4 5 6

Replacing a Pump
4. Disconnect the subsystem tubing between the pump head and the high-pressure valve as
follows:
Note The PLF pump can have an internally or an externally threaded pump head.
The latest version of the PLF pump has an internally threaded pump head.
a. Disconnect the tubing from the pump head as follows:
• If a PEEK fitting is connected to the pump head, use a 13 mm open-ended

wrench to remove it (see Figure 165).
Figure 165. Externally threaded pump head for a PLF model pump
PEEK fitting connected

to an externally threaded
pump head
• If a stainless steel fitting is connected to the pump head (see Figure 166), use a
1/4 in. open-ended wrench to remove it.
Figure 166. Internally threaded pump head for a PLF model pump

connected to an
internally threaded
pump head

Replacing a Pump
b. While holding the pressure sensor, use a 1/4 in. open-ended wrench to disconnect the
tubing connected to the pressure sensor’s inlet and outlet ports (see Figure 167).
Figure 167. Disconnecting the solvent lines from the pressure sensor
Solvent lines connected

c. Using a 1/4 in. open-ended wrench, disconnect the other end of the tubing that is
connected to the subsystem valve as follows:
• For valve S, disconnect the tubing from port 6.
• For valve A or B, disconnect the tubing from port 1.
5. Disconnect the pressure sensor assembly and the damaged PLF pump from the
instrument panel as follows:
a. Using a 2.5 mm L-hex wrench or ball driver, remove the two hex screws that secure
the pressure sensor L bracket to the instrument panel (see Figure 168). Then set the
two 2.5 mm hex screws aside for reuse when you reconnect the L bracket to the
instrument panel.
b. Using a 2 mm L-hex wrench or ball driver, unscrew the two hex screws that secure the
pressure sensor to the L-bracket (see Figure 168). Then set the L-bracket and the
two 2 mm hex screws aside for reuse when you mount the new pressure sensor.
Figure 168. Pressure sensor L-bracket screws
2.5 mm ball driver
Screws that secure

the pressure sensor
to the L bracket
Screws that secure
the L bracket to the
instrument panel

Replacing a Pump
c. Disconnect the P-Bus communication cables from the pump actuator

(see Figure 169).
Figure 169. Disconnected P-Bus communication cable
P-Bus
communication
cable
d. Using a 3 mm ball driver or L- hex wrench, remove the four screws that secure the
pump to the instrument panel (see Figure 170).
e. Set the four 3 mm screws aside for reuse in step 8a on page 159.
Figure 170. Removing the four screws that secure the pump to the instrument panel
3 mm driver
6. Install the new pressure sensor as follows:

a. Using a 2.0 mm L-hex wrench or ball driver and the two 2.0 mm hex screws that you
set aside when you disconnected the original pressure sensor from the L-bracket,
connect the new pressure sensor to the L-bracket.
b. Using a 2.5 mm L-hex wrench or ball driver and the two 2.5 mm hex screws that you
set aside when you removed the L-bracket from the instrument panel, reconnect the
L-bracket to the instrument panel.
7. If you are replacing pump S in an early version of the EASY-nLC II instrument, install the
components supplied in the Pump Mounting Kit as described in “To install the bracket
and adapter plate provided in the Pump Mounting Kit” on page 160. Then continue this
installation at step 9.

Replacing a Pump
8. Connect the new pump as follows:

a. Using a 3 mm ball driver or L-hex wrench and the four 3 mm hex screws that you set
aside when you removed the damaged pump from the instrument, secure the new
pump to the instrument panel.
b. Connect the pressure sensor cable from the new pressure sensor to the receptacle on
the right side of the PLU pump.
c. Connect the P-Bus communication cables.
9. Check the address setting for the rotary switch. If necessary, use a small flathead
screwdriver to change the rotary switch address on the new pump PCB.
• Pump A =1
• Pump B = 2
• Pump S = 3
10. Install tubing from the pump to the pressure sensor and from the pressure sensor to the
valve. Use PEEK tubing for subsystems A and S. Use stainless steel tubing for
subsystem B.
11. Reconnect the power cable to the instrument’s back panel, and turn on the
12. Prime the new pump as described in “Priming the Pump” on page 71.
13. Remove air from the system as described in “Removing Air After Replacing a Piston Seal
or a Pump” on page 73.
14. Make sure that both the right and left instrument panels have been installed and that the
instrument has been turned on for at least 30 minutes.
15. Run the flow sensor calibration for the new pump (see “Calibrate – Flow Sensors” on
page 51).
16. If you replaced pump S, run the Sample Pickup script (see “Test – Sample Pickup” on
page 42).
The instrument is now ready for use.

Replacing a Pump
 To install the bracket and adapter plate provided in the Pump Mounting Kit
Note Some earlier versions of the EASY-nLC II instrument cannot accommodate a

PLU pump in the pump S position without modification.
To provide space for the pump outlet tubing in these instruments, you must install
the new flow sensor bracket and the pump adapter plate supplied in the Pump
Mounting Kit. The new flow sensor bracket places the flow sensors in a higher
position and the pump adapter plate places the pump in a lower position than their
original positions on the instrument panel. This repositioning makes space for the
tubing that is connected to the pump head.
1. If you have not already done so, follow step 1 on page 154 through step 6 on page 158 of
the previous procedure, “To replace a PLF pump with a PLU pump in the EASY-nLC II
instrument,” to upgrade the touch-screen software, gain access to the solvent system
compartment, remove the damaged pump, and replace the pressure sensor.
2. Disconnect the tubing from the inlet and outlet ports of the flow sensors.
3. Replace the flow sensor bracket with the new flow sensor bracket supplied in the Pump
Mounting Kit as follows:
a. Using a 2.5 mm hex wrench, remove the two screws that secure the flow sensor
bracket to the instrument panel (see Figure 171).
b. Set the two 2.5 mm screws aside for reuse when you secure the new flow sensor
bracket.
Figure 171. Removing the two screws that secure the flow sensor bracket to the panel
2.5 mm hex wrench
c. Using a 2.0 mm hex wrench or ball driver, remove the four screws that secure the two
flow sensors to the flow sensor bracket (see Figure 172).
d. Set the 2.0 mm hex screws aside for reuse when you secure the flow sensors to the
new flow sensor bracket.

Replacing a Pump
Figure 172 shows the four 2.0 mm hex screws that secure the flow sensors to the flow
sensor bracket and the original flow sensor bracket. Figure 173 shows the flow sensors
removed from the flow sensor bracket. The flow sensor cables are still connected to
the instrument.
Figure 172. Screws that secure the flow sensors to the bracket
Two screws per flow sensor
Figure 173. Flow sensors removed from the flow sensor bracket
e. Using a 2.5 mm hex wrench and the screws that you set aside when you removed the
flow sensors from the original flow sensor bracket, connect the flow sensors to the
new flow sensor bracket supplied in the Pump Mounting Kit.
Note The mounting holes in the new flow sensor bracket are lower than the
mounting holes in the original flow sensor bracket. When you connect the new
bracket to the instrument panel, it is positioned higher than the original bracket,
allowing more space for the tubing that is connected to the pump head.
Figure 174. New flow sensor bracket (with lower mounting holes)
Lower mounting holes in the new

flow sensor bracket

Replacing a Pump
4. Using a 2.5 mm hex wrench and the screws that you set aside when you removed the
original flow sensor bracket from the instrument panel, connect the new flow sensor
bracket to the instrument panel.
5. Reconnect the tubing to the inlet and outlet ports of the flow sensors. Be careful when
installing the fused silica line to flow sensor B, as the end of the tubing is fragile.
CAUTION Take care when you connect the fused-silica line to the outlet port of
flow sensor B. The end of the tubing is fragile and easily damaged.
6. Using a 2.5 mm L-hex wrench or ball driver and the four screws provided in the Pump
Mounting Kit, secure the pump adapter plate to the instrument panel.
Figure 175. Securing the pump adapter plate to the instrument panel
Pump adapter plate
7. Install the PLU pump in the pump S position as follows:

a. Using a 3 mm ball driver or L-hex wrench and the four 3 mm hex screws that you set
aside when you removed the damaged pump from the instrument panel, secure the
new pump to the pump adapter plate.
b. Connect the pressure sensor cable from the new pressure sensor to the receptacle on
the right side of the PLU pump.
c. Connect the P-bus communication cables.
8. To complete the pump installation, start from step 9 on page 159 of the previous
procedure, “To replace a PLF pump with a PLU pump in the EASY-nLC II instrument.”

Replacing a Pump PCB

The procedure for replacing the pump PCB differs between the PLU model pump and the
PLF model pump.
Note The PLU pump is standard in the EASY-nLC 1000 instrument. The PLF pump is
standard in most EASY-nLC II instruments. Figure 8 on page 9 shows these two pump
models.
To replace a pump PCB, follow the appropriate procedure:

• “Replacing a Pump PCB in the PLU Pump,” on this page
• “Replacing a Pump PCB in the PLF Pump” on page 167
Replacing a Pump PCB in the PLU Pump

Replacing the pump PCB on the PLU model pump requires these items.
Tools Parts
• #2 Phillips screwdriver Pump PCB, P/N LC574
To replace the pump PCB on the PLU pump, follow these steps:
1. “To remove a pump PCB from the PLU model pump,” on this page
2. “To replace a pump PCB on the PLU model pump” on page 166
 To remove a pump PCB from the PLU model pump
1. Close down the EASY-nLC 1000 instrument as described in “Closing Down the
EASY-nLC Instrument” on page 21.
4. Disconnect the P-Bus communication cables, the flow sensor cable, and the pressure
sensor cable from the pump.
Figure 176 on page 164 shows these cables connected to the pump.

5. Using a 2.5 mm L-hex wrench or ball driver, loosen the four captive screws on the PCB
shield (see Figure 176). Then remove the PCB shield (see Figure 177).
Figure 176. Four PCB shield screws (PLU model pump)
Flow sensor cable
Pressure sensor cable
P-Bus cables
The four captive screws remain in place (see Figure 177).

Figure 177. Removing the PCB shield (PLU model pump)

6. Slide the PCB forward and away from the four mounting studs.
7. Disconnect the motor cable on the back of the pump PCB (see Figure 178).
Figure 178. Motor cable connected to the pump PCB (PLU model pump)
Motor cable

 To replace a pump PCB on the PLU model pump
1. Using a small flathead screwdriver, reset the address on the rotary switch on the pump
PCB (see Figure 179) as follows:
• Pump A =1
• Pump B = 2
• Pump S = 3
Figure 179. PCB rotary switch
PCB rotary switch
2. Plug the motor cable into the back of the PCB (see Figure 178 on page 165).
3. Insert the new pump PCB onto the pump.
4. Install the PCB shield.
5. Using a 2.5 mm L-hex wrench or ball driver, tighten the four 2.5 mm hex screws in the
PCB shield.
6. Reconnect the P-Bus communication cables, the flow sensor cable, and the pressure
sensor cable (see Figure 176 on page 164) to the pump.
8. Reconnect the power cable to the back panel of the instrument.
9. Turn on the instrument.
10. Wait for 30 minutes to allow the temperature in the housing to stabilize.
11. Calibrate the flow sensor by following the automated script described in “Calibrate –
Flow Sensors” on page 51.

Replacing a Pump PCB in the PLF Pump

Replacing a pump PCB (PLF model pump) in the EASY-nLC II instrument requires these
items.
Tools Parts
• #2 Phillips screwdriver Pump PCB, P/N LC274
To replace the PCB on a PLF pump, follow these steps:

1. To remove the pump PCB from the PLF model pump (EASY-nLC II instrument)
2. To install the pump PCB on a PLF pump (EASY-nLC II instrument)
 To remove the pump PCB from the PLF model pump (EASY-nLC II instrument)
1. Close down the EASY-nLC II instrument as described in “Closing Down the EASY-nLC
Instrument” on page 21.
4. Disconnect the P-Bus communication cables (see Figure 169 on page 158) from the
pump actuator.
5. Unscrew and remove the four 2.5 mm hex screws that connect the PCB to the pump.
6. Disconnect the pressure sensor grounding cable (yellow wire).
7. Gently slide the PCB outward and turn it around to gain access to its back side.
8. Disconnect the pressure sensor communication cable. Take care to avoid putting any
stress on the cables.
9. Disconnect the motor cable. Again, take care to avoid putting any stress on the cables.
10. Remove the PCB.
11. Go to the next procedure “To install the pump PCB on a PLF pump (EASY-nLC II
instrument).”

 To install the pump PCB on a PLF pump (EASY-nLC II instrument)
1. Remove the damaged PCB as described in the previous procedure, “To remove the pump
PCB from the PLF model pump (EASY-nLC II instrument)” on page 167.
2. Using a small flathead screwdriver, reset the address on the rotary switch on the new
pump PCB as follows:
• Pump A =1
• Pump B=2
• Pump S=3
3. Reconnect the motor cable to the back of the PCB (see Figure 178 on page 165).
4. Mount the new PCB onto the pump.
5. Secure the PCB to the pump as follows:
• Slide the four screws into the holes in the four corners of the PCB.
• Slide the connector at the end of the pressure sensor grounding cable under the screw
in the lower-right corner of the PCB.
• Using a 2.5 mm hex wrench, tighten the four screws.
Figure 180. PLF pump with the pressure sensor cable connected
0 1
9
2 3
7 8
4 5 6
Pressure sensor
grounding cable
P-Bus cable P-Bus cable

Motor cable routed
to the back of the PCB
CAUTION To avoid damaging the PCB, make sure that the grounding connector does
not touch any other components.
6. Reconnect the P-Bus communication cables.

7. Calibrate the flow sensor by following the automated script described in “Calibrate –
Flow Sensors” on page 51.

6
Troubleshooting
To troubleshoot problems with the EASY-nLC instrument, follow the troubleshooting tips
and procedures in this chapter.
Contents
• Troubleshooting Tips
• Using the Direct Controls for Troubleshooting and Maintenance
• Troubleshooting a Pump that Fails the Flush Air Script
• Troubleshooting a Pump that Fails the Leaks Script
• Running a System Leak Test
• Troubleshooting the Results of the System Leak Test
• Identifying a Leaking Check Valve
• Troubleshooting a System Blockage
• Troubleshooting the Autosampler Aspiration and Calibration
• Checking Sample Pickup
• Troubleshooting Communication Problems
• Verifying that the LC/MS System Is Properly Grounded

6 Troubleshooting
Troubleshooting Tips
To troubleshoot problems with the EASY-nLC instrument, see these topics:
• “Autosampler Problems” on page 171
• “Contact Closure Problems” on page 172
• “Instrument Startup Problems” on page 172
• “Delayed Elution” on page 173
• “Excessive Duration or Higher Pressure for the Column Equilibration and Sample
Loading Steps” on page 178
• “System Reaches Its Maximum Pressure During the Gradient” on page 180
• “Sample Signal Weak or Absent” on page 183
• “Slow or No Pressure Increase in Subsystem A or B” on page 187
• “Errors Reported by the Xcalibur Data System” on page 189
• “Carryover” on page 194
• “Spray Issues” on page 196
• “Chromatographic Performance” on page 197
• “Device Failures” on page 198
• “Miscellaneous” on page 202

6 Troubleshooting
Autosampler Problems
Table 9 lists troubleshooting tips for the autosampler.
Note For information about troubleshooting sample pickup, see “Troubleshooting the
Autosampler Aspiration and Calibration” on page 261.
Table 9. Autosampler troubleshooting tips

Symptom Possible causes Action
The needle cannot The needle tip is damaged or Do the following:
penetrate the plastic bent.
1. Check the software configuration for the adapter tray.
film on the microtiter
plate. 2. Eject the tray.
3. Remove the left side panel and visually inspect the
needle tip.
• If the needle tip is bent or damaged, replace it
(see “Replacing the Autosampler Needle” on
page 84).
• If there is any residue on the needle tip, wipe the
needle tip with a lint-free tissue soaked in
LC/MS-grade ethanol.
XYZ robot error Possible step loss on one of Remove the obstacle and try again. You might need to
the motors because the calibrate the autosampler for more precise penetration of
movement of the autosampler’s the microtiter plate or the wash bottles.
XYZ arm is blocked
For information about calibrating the autosampler, see
Chapter 7, “Calibrating the Autosampler’s XYZ Robot.”
The error repeats without any Contact Thermo Fisher Scientific:
visible reason.
• us.customer-support.analyze@thermofisher.com
• eu.techsupport.cms@thermofisher.com
A server warning The plate format has been If you want to run the batch, you must create the plate
message about the plate deleted from the system format again.
format for the configuration. For information
autosampler about deleting a plate format, For information about selecting, creating, and deleting
configuration pops up refer to the EASY-nLC Series plate formats, see “Managing Plate Formats” on page 274
when you submit a Getting Started Guide.
batch.

6 Troubleshooting
Contact Closure Problems

Table 10 contains troubleshooting tips for contact closure problems.
Table 10. Contact closure troubleshooting tips
The mass spectrometer is Incorrect contact closure If you are running two-way contact closure (with
waiting for a contact closure setup feedback from the mass spectrometer), set the contact
signal. closure Protocol setting to Two-way on the
Configuration > Connections page.
If the mass spectrometer is waiting for a signal, set the

contact closure State setting to Open.
The EASY-nLC instrument If you are running one-way contact closure (that is,
is waiting for a ready signal the EASY-nLC instrument sends a start signal to the
from the mass spectrometer. mass spectrometer, but feedback from the mass
spectrometer is ignored), set the contact closure
Protocol setting to One-way on the Configuration >
Connections page.
Instrument Startup Problems

Table 11 contains troubleshooting tips for instrument startup problems.
Table 11. Startup troubleshooting tips
Dark monitor Broken or open main 1. Turn on the power to the instrument.
power fuse
2. Remove the right side panel of the EASY-nLC instrument.
3. If there is no light on the pumps, turn off the EASY-nLC
instrument, replace the right side panel, and check the fuse.
Defective monitor Attach an external monitor to the VGA connector (labeled
MONITOR) on the back panel of the instrument (see Figure 16
on page 16).
Startup bar is no longer Damaged instrument Turn off the EASY-nLC instrument, wait 5 seconds before turning
proceeding. it on again, and then wait approximately 10 minutes for the
restart process to finish. In some cases this recovers the system.
Contact Thermo Fisher Scientific if the problem recurs:
• us.customer-support.analyze@thermofisher.com
• eu.techsupport.cms@thermofisher.com

6 Troubleshooting
Delayed Elution
The most common cause of delayed elution is a worn rotor seal in valve B, causing valve B to
leak.
Table 12 lists the common causes of delayed elution. These topics show the effect of leaks and
swept volume on the pressure and flow traces:
• “Leaks that Cause Delayed Elution” on page 174
• “Introduced Swept Volume” on page 176
Table 12. Common causes of delayed elution
Symptom Possible cause Action
Delayed elution Leak in the solvent system 1. Run the Leaks script for the system (see “Test – Leaks” on
page 44).
2. Locate the leak by following “Troubleshooting the Results
of the System Leak Test” on page 221.
Incorrect tubing installed 1. Remove the right side panel of the instrument.
2. Verify that the tubing matches the solvent system
schematic.
• For the EASY-nLC II instrument, see page 314.
• For the EASY-nLC 1000 instrument, see page 316.
3. Replace the incorrect tubing with the specified tubing.
Swept volume introduced Check the tubing connections.
by incorrect tubing
connections In the EASY-nLC II instrument, you can inadvertently
introduce swept volume (extra volume in the solvent path) by
not seating the tubing against the bottom of the receiving
port.

6 Troubleshooting
Leaks that Cause Delayed Elution

When there is a leak in the system upstream from flow sensor B, part of the solvent stream
from pump A exits the mixing Tee toward flow sensor B, pushes solvent B back toward
valve B, and partly fills the solvent line between the mixing Tee and flow sensor B during the
column equilibration and sample loading steps (see Figure 181).
When the gradient step begins, instead of pushing solvent B into the mixing Tee, pump B
initially pushes this small volume of solvent A, delaying the start of the actual gradient.
Figure 181. Negative flow of solvent B toward valve B during the column equilibration and sample loading steps
Pressure Mixing Tee

sensor Positive flow
↓
Pump B
1
2 6
3 4 5 Flow sensor A
Valve A
Pressure
sensor Negative flow
Pump B
↓
1
2 6
Flow sensor B
3 4 5
Valve B
A leak in valve B or the solvent line between

valve B and flow sensor B can allow solvent A
to enter the solvent path between the mixing
Tee and valve B during the column
equilibration and sample loading steps.

6 Troubleshooting
Figure 182 shows the flow and pressure traces for pump B for a system with a leak upstream of
flow sensor B. The measured flow rate is negative rather than 0 nL/min during the column
equilibration and sample loading steps.
Figure 182. Flow trace for pump B when there is a leak upstream of flow sensor B
Negative flow rate during the

column equilibration and sample
loading steps

6 Troubleshooting
Introduced Swept Volume

Normally when solvent B (acetonitrile with 0.1% formic acid) reaches the column, the back
pressure measured by pressure sensor A drops to less than one-half the amount measured for
solvent A (water with 0.1% formic acid) alone. If the back pressure does not drop by more
than 50 percent when solvent B reaches the column, the solvent system might contain
additional swept volume introduced by poor tubing connections.
The additional swept volume increases the gradient delay volume so that the gradient reaches
the column later.
Figure 183 shows the pressure dip that occurs when the gradient starts to reach the column.
Figure 184 shows the pressure dip for the sample chromatographic method, but occurring
two minutes later due to the added gradient delay volume.
Figure 183. Normal pressure dip for pressure sensor A as the gradient reaches the column
The pressure starts

to drop at approximately
25 minutes as 100%
solvent B reaches
the column.

6 Troubleshooting
Figure 184. Pressure dip begins later when the system has introduced swept volume
The pressure starts

to drop at approximately
27 minutes as
100% solvent B
reaches the column.
Back pressure is proportional to the viscosity of the solvent mixture. If you are not running a
water/acetonitrile gradient, the pressure profile of your gradient run will differ.
Table 31 on page 311 lists the viscosities for two-solvent mobile phases consisting of a
water/methanol mixture or a water/acetonitrile mixture.

6 Troubleshooting
Excessive Duration or Higher Pressure for the Column Equilibration and Sample
Loading Steps
Table 13 lists possible causes for the following:
• When the column equilibration and sample loading steps are controlled by a specified
pressure, the duration of these steps is longer than expected.
• When these steps are controlled by a specified flow, the pressure is higher than expected
during the column equilibration step, the sample loading step, or both steps.
During the sample loading and column equilibration steps, pump A delivers the user-specified
volume of solvent A to the system at the user-specified flow rate or maximum pressure or the
maximum system pressure. When the columns or the Column Out line is clogged, the system
must lower the flow rate to maintain the pressure at the maximum pressure specified in the
method. The lower flow rate increases the column equilibration time, the sample loading
time, or both.
Table 13. Common causes of a longer than expected column equilibration time or sample loading time
When the method specifies a set Clogged column Run the Back Pressure script for pump A
flow rate for the column (see “Test – Back Pressure” on page 48).
equilibration, sample loading, or
both of these steps, the pressure is If the test passes, one of the columns is
higher than usual. probably clogged and must be replaced.
Clogged system Run the Back Pressure script for pump A.
When the method specifies a
maximum pressure for one or both If the test fails, go to “Troubleshooting a
of these steps, the duration of these System Blockage” on page 249.
steps is longer.
Figure 185 and Figure 186 show the flow rate and pressure traces for pump A for a normal
run and a run with a partially clogged column, respectively. The flow rate for a run with a
clogged column is lower than the flow rate for a normal run. The lower flow rate increases the
duration of the column equilibration and sample loading steps.
Note The specifications for the precolumns used to acquire the data in
Figure 185 and Figure 186 are as follows:
• 2 cm length
• 100 μm ID
• 5 μm particle size
• C18

6 Troubleshooting
Figure 185. Normal run
Sample loading step (10 μL/min)
Precolumn equilibration step (10 μL/min)
Figure 186. Run with a partially blocked column
Sample loading step (4 μL/min)
Precolumn equilibration step (3.5 μL/min)

6 Troubleshooting
System Reaches Its Maximum Pressure During the Gradient

If the pressure trace shows maximum pressure during the gradient, review the possible causes
in Table 14.
Table 14. Possible causes of maximum pressure spikes during a run
The system reaches its Clogged column Run the Back Pressure script for pumps A and B.
maximum pressure during a
If the test passes, one of the columns is probably
run.
clogged and needs to be replaced.
Clogged system Run the Back Pressure script for pumps A and B.
If the test fails, go to “Troubleshooting a System
Blockage” on page 249.
Excessively high flow rate Reduce the flow rate in the method.
When a column or the Column Out line is clogged, the back pressure can increase to the
maximum system pressure for pump A, pump B, or pumps A and B during the gradient
(see Figure 187).
Figure 187. Back pressure shown reaching the maximum system pressure for pumps A and B
Maximum pressure Maximum pressure
reached for pump A reached for pump B

6 Troubleshooting
When only the flow path between pump B and the mixing Tee has a blockage, the
back pressure on pump B increases and differs from the back pressure on pump A.
Figure 188 shows the typical profile for a blockage in the solvent system between pump B and
the mixing Tee.
Figure 188. Back pressure shown reaching the maximum pressure for pump B only
Maximum
pressure reached
for pump B

6 Troubleshooting
Figure 189 shows the flow path between pump B and the mixing Tee.
Figure 189. Solvent lines between pump B and the mixing Tee
Valve B
Mixing Tee
1 2
Pressure
sensor
Pump B
3
↓
1
2 6 4
Flow sensor B
Connected to 3 4 5
check valve assembly B
No. EASY-nLC II instrument EASY-nLC 1000 instrument

1 Stainless steel tubing and fittings Stainless steel tubing and fittings
2 Stainless steel tubing and fittings Stainless steel tubing and fittings
3 PEEKsil tubing nanoViper
• Stainless steel fitting connected to port 6 of valve B
• PEEK fitting connected to the flow sensor inlet
4 Fused-silica solvent line nanoViper
• PEEK fitting connected to the flow sensor outlet
• PEEK fitting connected to the mixing Tee

6 Troubleshooting
Sample Signal Weak or Absent

If the sample signal is missing or weak, review the troubleshooting tips in Table 15.
Table 15. Possible causes of a weak or absent signal
The sample signal is missing or Sample not aspirated Run the Sample Pickup script. If the Sample
weak. (See Figure 190 on page 184.) Pickup script fails, see “Troubleshooting the
Autosampler Aspiration and Calibration” on
page 261.
Damaged or incorrect column Make sure that you have installed the correct
(See Figure 191 on page 185.) column or columns.
Check the back pressure on the columns by

running the column equilibration scripts.
Leak in the system Run the Leaks test on the system.
(See Figure 192 on page 186.)
If the test fails, see “Troubleshooting the Results
of the System Leak Test” on page 221.
Incorrect column configuration Check the column configuration.
2. In the Devices list, select EASY-nLC
(HPLC).
3. Press the Properties tab.
4. Clear the One Column Setup check box for
a two-column setup or select this check box
for a one-column setup.
For more information, refer to the EASY-nLC

Series Getting Started Guide.
Incorrect solvent in W3 bottle Make sure that the W3 bottle contains solvent A.
Incorrect sample loop Check the loop configuration on the Properties
configuration page for the EASY-nLC HPLC device on the
Maintenance > Devices page.
Make sure that the configured loop volume

matches the installed sample loop.

6 Troubleshooting
Weak or Absent Signal—Sample Not Aspirated

A pressure drop at the start of the sample loading step indicates that pump S has introduced
air into the sample loop (see Figure 190).
When the method uses pressure to control the flow rate, the pressure should return to the
specified level within approximately 4 seconds after the sample is loaded onto the column. If
the pressure does not return to the specified level within approximately 4 seconds, pump S has
probably introduced air into the system.
Figure 190. Typical pump A profile for a system with air in the sample loop
Pressure drop at the start of the

Sample Loading step

6 Troubleshooting
Weak or Absent Signal—Defective Precolumn

When compared to the Pump A graph for a normal run shown in Figure 185 on page 179,
Figure 191 shows the reduced time for the precolumn equilibration and sample loading steps
when the precolumn is damaged and has lost a significant portion of its packing material.
The flow rate for the column equilibration and sample loading steps is higher (>15 μL/min)
and the duration is shorter because the precolumn is exerting less back pressure.
Note The specifications for the precolumns used to acquire the data in
Figure 185 and Figure 186 are as follows:
• 2 cm length
• 100 μm ID
• 5 μm particle size
• C18
Figure 191. Typical pump A profile for a damaged precolumn

The measured flow rate
is > 15 μL/min.
Sample loading step
Column equilibration step

6 Troubleshooting
Weak or Absent Signal—Leak Upstream of Flow Sensor B

Figure 192 shows a typical pump B profile for a system with a leak upstream of flow sensor B.
Flow sensor B displays a negative flow during the column equilibration and sample loading
steps.
If the gradient is short, a leak upstream of flow sensor B will cause a complete lack of signal
because solvent B is not reaching the columns within the duration of the gradient.
Figure 192. Typical pump B profile for a leak upstream of flow sensor B
Negative flow during the

column equilibration and
sample loading steps

6 Troubleshooting
Slow or No Pressure Increase in Subsystem A or B

A lack of pressure or a slow increase in pressure in subsystem A or B is often caused by a worn
piston seal, a worn rotor seal, or a leaking tubing connection.
Note A subsystem includes the pump, the solvent line that connects the pump to the
pressure transducer, the solvent line that connects the pressure transducer to the valve, and
the valve.
Table 16. Troubleshooting low back pressure in subsystems A or B

Back pressure is Air in the pump Run the Purge Solvent script for the affected pump with 2 iterations.
low in subsystem A Then, run the Flush Air script. If the Flush Air script fails, see
or B. “Troubleshooting a Pump that Fails the Flush Air Script” on page 212.
Leak in the pump Run the Leaks script for the affected pump. If the Leaks script fails, see
“Troubleshooting a Pump that Fails the Leaks Script” on page 216.
Figure 193 shows the leak test profile for pump A. Even when the flow rate is set to the
maximum allowable value, the pressure for pump A does not increase.
Figure 193. Leak test profile for pump A
Extremely low pressure

6 Troubleshooting
When subsystem A has a large leak, pump A can run out of solvent during a sample run,
resulting in the server error message shown in Figure 194.
Figure 194. Server error message displayed when pump A runs out of solvent
When subsystem B has a large leak or is filled with air, the gradient fails to start because the
pressure cannot be increased to reach the starting conditions (see Figure 195).
Figure 195. Subsystem B leak
Pressure
remains
low

6 Troubleshooting
When pump B cannot generate sufficient pressure to start the gradient, the server error
message shown in Figure 196 appears.
Figure 196. Server error message displayed when pump B cannot generate sufficient pressure to
start the gradient
Errors Reported by the Xcalibur Data System

Table 17 lists the possible causes of the common errors reported by the Xcalibur data system.
Table 17. Possible causes of errors reported by the Xcalibur data system (Sheet 1 of 2)
An Acquisition Server failure Lost connection between the Check the Ethernet connections between the
prevents the sequence from running EASY-nLC instrument and the EASY-nLC instrument and the data system
(see Figure 197 on page 190). external data system computer computer.
Exit the Xcalibur data system. Then, open

the Thermo EASY-nLC Configuration
dialog box and click Test Connection.
If necessary, restart the EASY-nLC system.

The Acquisition Server displays the Injection volume is greater than Check the loop configuration on the
message that the EASY-nLC device the loop size minus 2 μL Properties page for the EASY-nLC HPLC
has reported a failure during the device on the Maintenance > Devices page.
Prepare For Run step. (See Figure 198 on page 191.)
Make sure that the configured loop volume
matches the installed sample loop.
Lowercase letter used in the Change the letters to capitals.
sequence table for vial position
(See Figure 199 on page 191.)

Unable to submit samples. The Incorrect plate configuration Select the correct autosampler plate in the
following error message appears: Thermo EASY-nLC Configuration
Invalid Autosampler Vial Position (See Figure 200 on page 192.) dialog box.

6 Troubleshooting
Table 17. Possible causes of errors reported by the Xcalibur data system (Sheet 2 of 2)
The mass spectrometer remains in Contact closure configured Press Configuration > Connections.
the Waiting for Contact Closure incorrectly
state and data acquisition does not Select the correct MS configuration and
start (see Figure 201 on page 193). settings.
Failing contact closure relay Check accordingly to “Verifying that the
due to incorrect grounding LC/MS System Is Properly Grounded” on
page 268.
Figure 197 shows the Acquisition Server message that appears when the EASY-nLC
instrument loses communication with the data system computer during a sequence run. The
sequence pauses until you intervene.
Figure 197. Lost connection between the EASY-nLC instrument and the Acquisition Server

6 Troubleshooting
Figure 198 shows the Acquisition Server message that appears during the Prepare for Run step
when the requested injection volume is greater than the configured loop size minus 2 μL.
Figure 198. Incorrect injection volume
A requested injection volume of
20 μL is too large for a 20 μL loop.
Figure 199 shows the Acquisition Server message that appears when you incorrectly use a
lowercase letter to define the vial or well position. For the EASY-nLC device, you must use
capital letters in the alphanumeric description of the vial or well position.
Figure 199. Incorrect vial position nomenclature
Incorrect use of a lowercase letter

6 Troubleshooting
Figure 200 shows the Home Page error message that appears when the sequence list contains a
well plate position and the autosampler configuration is set up for the vial adapter plate
format.
Figure 200. Incorrect vial position for the vial adapter plate format
Invalid vial position

6 Troubleshooting
Figure 201 shows that the mass spectrometer is waiting for a start signal from the EASY-nLC
device before it starts data acquisition. The mass spectrometer remains in the Waiting for
Contact Closure state until it receives the start signal. The EASY-nLC instrument sends the
start signal when the run gradient step begins.
Figure 201. Waiting for Contact Closure error
Mass spectrometer state
EASY-nLC method step

6 Troubleshooting
Carryover
Table 18 lists the possible causes of carryover.
Table 18. Possible causes of carryover
Carryover from one run to the Incomplete elution of peptides Add extra time to the end of the gradient or add
next from column a high-organic hold to the end of the gradient.
To determine if the high-organic hold is long

enough, make sure that you see a pressure drop
during the hold period (see Figure 202 and
Figure 203).
Insufficient washing of needle Add extra wash steps to the method. Consider
and loop using an organic solvent for one of the custom
wash solvents.
Dead volumes in the column Remake the connections in the column setup.
setup
Figure 202 shows a gradient run with a high-organic hold at the end of the run that is too
short for the column to see the high-organic solvent, as displayed by the lack of a pressure
drop at the end of the run.
Figure 202. Gradient run without an adequate high-organic hold at the end of the run

6 Troubleshooting
Figure 203 shows the effect of a high-organic hold at the end of the gradient run on pressure.
The pressure continues to drop until the column equilibrates to the high-organic content.
Figure 203. Gradient run with an adequate high-organic hold at the end of the run
The gradient reaches
100% solvent B.
The pressure begins

to drop when the
high-organic mobile
phase reaches the
column.

6 Troubleshooting
Spray Issues
Table 19 lists the possible causes of an unstable spray.
Table 19. Possible causes of an unstable spray
Unstable spray Post-column outgassing Degas the solvents.
Poor connection in either the Check all of the connections.
liquid junction or the
DirectJunction
Incorrect MS settings or emitter Optimize the MS tune file for the desired
position flow rate and the emitter position.
Dirty emitter Clean the emitter with an organic solvent
such as methanol, acetonitrile, or ethanol.
Use only LC/MS-grade solvents.

Poor high-voltage connection Check all of the high-voltage connections.
Reconnect as necessary.
Air movement from an air Deflect the air from the vent, or use a shield
conditioning vent to protect the ion source.

6 Troubleshooting
Chromatographic Performance
Table 20 lists troubleshooting tips for common chromatography problems.
Table 20. Troubleshooting tips for chromatographic performance
Broad peaks Dead volume between the Check the connections.
column and emitter
Replace the fittings if needed.
Damaged column Inspect the column, especially the outlet.
Replace the column if it is damaged.

Poor retention time reproducibility Temperature fluctuations in the Monitor the laboratory temperature.
laboratory
Stabilize the temperature by keeping the
laboratory doors closed and by ensuring that
the air conditioning system is kept constant
at all times.
Do not run the EASY-nLC instrument with

the panels removed.
Back flow on flow sensor B Run the Leaks script for Pump A, Pump B,
and System.
Replace defective piston seals, rotor seals,

and solvent lines as indicated.
Spikes seen in flow sensor B Use the scripts to check for a leak in the B
during valve shifts subsystem (Leak test Pumps A + B, and
System).
Replace defective seals, rotors, and solvent

lines as needed.

6 Troubleshooting
Device Failures
Table 21 lists troubleshooting tips for devices failures.
Table 21. Troubleshooting tips for device failures
The pump icon for a pump Communication failure Check that the
that is not functioning turns to the pump. cables are
a pink color on the Home > connected
Overview page. Could be the pump or correctly.
the PC BUS cable.
See Figure 204 on page 199.
The valve icon for a valve Communication failure Check that all of
that is not functioning turns to the valve. the cables are
a pink color on the Home > connected
Overview page. Could be the valve or correctly.
the PC BUS cable
See Figure 205 on page 200.
The autosampler icon turns Communication failure Check that all of
a pink color on the Home > on the cooling unit. the cables are
Overview page. connected
Could be the PC box, a correctly.
See Figure 206 on page 201. damaged cable, or a
loose connection.

6 Troubleshooting
A pump icon turns pink when the pump loses communication with the EASY-nLC computer.
The pumps are serially connected, so if pump B loses communication, all of the pumps lose
communication. Pump B is the first pump in the series.
Communication between the pumps and the embedded computer can be lost when the cables
are loose, when the embedded computer fails, or when the pump PCB fails.
Figure 204 shows the pink pump icons on the Home > Overview page.
Figure 204. Pink pump icons on the Home > Overview page

6 Troubleshooting
A pink valve icon means that the communication to the unit has been lost. Be aware that
the valves are serially connected, so a failing valve might cause other valve icons to turn pink as
well.
Communication between the valves and the embedded computer can be lost when the cables
are loose, when the embedded computer fails, or when the valve PCB fails.
Figure 205 shows the pink valve icons on the Home > Overview page.
Figure 205. Pink valve icons on the Home > Overview page

6 Troubleshooting
An autosampler icon turning pink means that the communication to the unit has been lost.
Figure 206 shows the pink autosampler icon on the Home > Overview page.
Figure 206. Pink autosampler icon on the Home > Overview page

6 Troubleshooting
Miscellaneous
For additional issues that might arise while using the EASY-nLC instrument, consult these
miscellaneous troubleshooting tips (Table 22).
Table 22. Miscellaneous troubleshooting tips (Sheet 1 of 2)
Copying log files to a USB Memory stick in wrong format Format the memory stick in FAT/FAT16 format.
memory stick failed.
Memory stick not recognized by Use one of the memory sticks supplied by
the instrument Thermo Fisher Scientific, or try plugging the
stick into the other USB port.
Contact Thermo Fisher Scientific if neither

action works: us.customer-support.analyze
@thermofisher.com
eu.techsupport.cms
@thermofisher.com
Copying to the USB memory Too much data to be copied Remove the memory stick from the EASY-nLC
stick does not stop. instrument and press Ignore when the error
message appears.
Contact Thermo Fisher Scientific for an

instrument check-up:
us.customer-support.analyze
@thermofisher.com
eu.techsupport.cms
@thermofisher.com
Forgot the admin password. If you are already logged in to the EASY-nLC
instrument, Thermo Fisher Scientific can extract
the password from the system in two ways:
• If the network is set up for remote access,
press Maintenance > Support and press
Connect.
–or–
• Run a factory reset.
System is running slower and Memory filled with graph data Press Home > Graph and disable the graphs by
slower. from long gradient run pressing No Graph in each graph window.
System overload caused by Restart the application or power down/power up
other reasons from Maintenance > Scheduling.

6 Troubleshooting
Table 22. Miscellaneous troubleshooting tips (Sheet 2 of 2)

Valve – unknown position The valve’ s duty cycle requires Run the Valve Check script (see “Test – Valve
calibration. Check” on page 47).
This script is only valid for EASY-nLC II

instrument valves with a serial number less than
V-009999.
Contact your local Thermo Fisher Scientific field

service engineer if the reported overshoot is
greater than 6.
Unhandled error or SVG Program error in the software In most situations you can continue your work
(scalable vector graphics) error release by pressing Ignore or OK. More serious error
situations might require restarting the HPLC.
To improve on the software quality, e-mail details

to:
us.customer-support.analyze
@thermofisher.com
eu.techsupport.cms
@thermofisher.com
Or, connect to the remote support server. See

“Connecting the EASY-nLC Instrument to the
Support Server” on page 288.

6 Troubleshooting
Using the Direct Controls for Troubleshooting and Maintenance

You can access the direct controls for the instrument’s hardware components by pressing the
component icons on the Home > Overview page.
These topics describe how to use the direct controls:

• Using the Valve Controls
• Using the Pump Controls
• Using the Autosampler Controls
Using the Valve Controls

You can change the positions of the instrument’s three-position valves from the
Home > Overview page. For information about the valve positions, see “Six-Port Rotary
Valves” on page 12.
 To change the position of a valve
1. On the Home > Overview page, press the valve icon for the valve that you want to
control.
The Valve dialog box opens (see Figure 207). The readback box lists the current valve
position.
Figure 207. Valve dialog box
Readback box
2. Press the button for the position that you want the valve to switch to: 1–2, Center,
or 1–6.
The readback box displays the new position.

6 Troubleshooting
Using the Pump Controls

You can refill and empty the pumps from the Home > Overview page.
IMPORTANT Use the pump’s direct controls for troubleshooting.

To avoid contaminating the pumps, take care when you use these controls:
• For pump A or B, make sure that its corresponding valve is in position 1–2 before you
refill the pump.
• For pump S, before you empty or fill the pump, use the autosampler’s direct controls
to insert the autosampler needle into the W4 or W3 bottle, respectively.
Tip To prepare the EASY-nLC instrument for operation, use the Prepare – Purge Solvent
script to flush the solvent lines (see “Prepare – Purge Solvent” on page 32). The Purge
Solvent script places the valves in the appropriate positions for filling and emptying
pumps A and B and places the autosampler needle in the appropriate wash and waste
bottles for filling and emptying pump S.
To work with the pump’s direct controls, follow these procedures:

• Opening the Direct Controls for the Pumps
• Using the Direct Controls To Fill or Empty Pump A or B
• Using the Direct Controls To Fill or Empty Pump S
Opening the Direct Controls for the Pumps

Each pump is represented by a pump icon on the Home > Overview page.
 To open the pump dialog box
On the Home > Overview page, press the pump icon for the pump that you want to
control.
Its dialog box opens (see Figure 208). The Position readback box displays the current
pump position from 0 μL (empty) to 140 μL (full).

6 Troubleshooting
Figure 208. Pump dialog box
Volume box Flow rate box
Readback boxes
Note Because pump S does not have an associated flow sensor, the Pump S dialog box
does not include a Real Flow readback box.
Using the Direct Controls To Fill or Empty Pump A or B

Before using the direct controls to fill or empty pump A or B, make sure that the valves are in
the appropriate position. For information about controlling the position of the valves, see
“Using the Valve Controls” on page 204.
IMPORTANT Before you fill pump A or B, make sure that the pump’s associated valve is
in position 1–2. You can contaminate the pump by attempting to fill the pump when its
associated valve is in position 1–6.
 To fill pump A or B with solvent
1. On the Home > Overview page, check the position of the valve that controls the solvent
flow direction for the pump of interest.
2. Make sure that the valve is set to position 1–2.
When valve A or B is in the 1–2 position, the corresponding pump draws solvent from
the solvent bottle on top of the instrument (see Figure 209).

6 Troubleshooting
Figure 209. Position of the rotary valve when filling a pump
Check valve assembly
Solvent bottle A
1
2 6
A
3 5
4
Waste beaker
Pump A
3. Press the pump icon for the pump you want to control.
The Pump dialog box opens (see Figure 208).
4. In the flow rate box, enter the filling flow rate: –0.01 to –300 μL/min.
For best results, enter a flow rate of –100 μL/min to fill the pump.
5. In the volume box, enter the volume that you want pump A or B to draw.
6. Press Start.
The pump draws solvent until it draws the requested volume or reaches the full position,
whichever occurs first.

6 Troubleshooting
 To empty pump A or B to waste
1. Check the position of the pump valve on the Home > Overview page.
• To empty pump A or B directly to waste, make sure that its valve is in position 1–2.
• To empty pump A or B to waste by way of valve W, place the pump valve in
position 1–6 and valve W in position 1–6.
Valve Position Solvent flow

A or B 1–2 Empties to the waste beaker.
1–6 Passes through valve S and into the Column Out line.
S 1–2 Bypasses the sample loop.
1–6 Passes through the sample loop.
W 1–2 Passes through the installed columns.
1–6 Exits the Column Out line to waste for a one column
setup or passes through the precolumn and then exits the
system to waste for a two-column setup.
3. Press the pump icon for the pump you want to control.
The Pump dialog box opens (see Figure 208 on page 206).
4. In the flow rate box, enter the flow rate: 0.01 to 300 μL/min.
When valve A or B is in position 1–6, the maximum system pressure limit constrains the
maximum flow rate.
5. In the volume box, enter the volume that you want the pump to empty to waste.
6. Press Start.
The pump empties until it pumps the requested volume or reaches the empty position,
whichever occurs first.

6 Troubleshooting
Using the Direct Controls To Fill or Empty Pump S

Before using the direct controls to fill or empty pump S, make sure that the autosampler
needle is inserted into the appropriate wash or waste bottle.
IMPORTANT To avoid contaminating pump S, take care to place the autosampler

needle in the appropriate wash bottle before filling the pump.
 To fill pump S
1. Make sure that a wash bottle with the appropriate solvent is installed in position W3.
2. Send the autosampler needle to the appropriate position as follows:
a. On the Home > Overview page, press the autosampler icon.
The Autosampler dialog box opens (see Figure 210 on page 210).
b. Press W3.
The autosampler needle moves to the W3 position.
c. Press Needle Down.
The autosampler needle descends into the W3 bottle.
d. Press Close to close the Autosampler dialog box.
3. Draw solvent into pump S as follows:
a. Press the pump S icon.
The Pump S dialog box opens.
b. In the flow rate box, enter the filling flow rate: –0.01 to –300 μL/min.
For best results, enter a flow rate of –40 μL/min to fill pump S.
c. In the volume box, enter the volume that you want pump S to draw.
d. Press Start.
The pump draws solvent until it draws the requested volume or reaches the full
position, whichever occurs first.
 To empty pump S to waste
1. Make sure that a wash bottle with a needle wash insert is installed in position W4.
2. Send the autosampler needle to the appropriate position as follows:
a. On the Home > Overview page, press the autosampler icon.
The Autosampler dialog box opens (see Figure 210 on page 210).
b. Press W4.
The autosampler needle moves to the W4 position.

6 Troubleshooting
c. Press Needle Down.

The autosampler needle descends into the W4 bottle.
d. Press Close to close the Autosampler dialog box.
3. Dispense solvent from pump S as follows:
a. Press the pump S icon.
The Pump S dialog box opens.
b. In the flow rate box, enter the flow rate: 0.01 to 300 μL/min.
c. In the volume box, enter the volume that you want the pump to empty to waste.
d. Press Start.
The pump empties until it pumps the requested volume or reaches the empty
position, whichever occurs first.
Using the Autosampler Controls

You can control the XYZ robot and the cooler temperature from the Home > Overview page.
 To open the Autosampler dialog box
Press the autosampler icon on the Home > Overview page.

The Autosampler dialog box opens (see Figure 210).
Figure 210. Autosampler dialog box
Vial or well position box
Temperature input box
Temperature readback box

6 Troubleshooting
 To start the calibration procedure for the current plate format
1. Press Goto Calibration.

The Tools view for the autosampler on the Maintenance > Devices page opens.
2. To calibrate the XYZ robot for the plate format, follow the instructions in “Calibrating
Plates” on page 280.
 To move the needle to a vial or well position
1. In the Vial or Well box, enter a vial or well position.

2. Press Goto.
 To move the needle to a wash bottle position
Press W1, W2, W3, or W4.
 To change the cooler temperature
1. Enter a temperature in the temperature input box.

2. Press Set.
3. Monitor the temperature change in the temperature readback box.

6 Troubleshooting
Troubleshooting a Pump that Fails the Flush Air Script

If pump A, B, or S fails the Flush Air script and the Output page displays one of the following
messages, a leak or blockage could be preventing solvent from entering the pump.
• Aborting unable to build pressure
• Aborting check solvent level
Note For information about the Flush Air script, see “Prepare – Flush Air” on page 33.
The following procedure systematically checks for a blockage in the check valve assembly, in
the solvent line that connects the pressure sensor to the valve, and in the pump head.
 To determine why the pump has failed the Flush Air script
1. If you have not already done so, remove the right side panel of the instrument.
2. Depending on the pump, do one of the following:
• For pumps A and B, go to step 3.
• For pump S, go to step 4 on page 213.
3. For pumps A and B, determine whether the check valve assembly is functioning as
follows:
a. Run the Purge script for the pump that has failed (see “Prepare – Purge Solvent” on
page 32).
b. Check that solvent is being aspirated and dispensed correctly through the Teflon™
lines.
• If the pump is drawing solvent during the fill portion of the purge cycle, the
solvent-side check valve is working properly.
• If the pump is dispensing solvent into the waste beaker during the empty portion
of the purge cycle, the waste-side check valve is working properly.
Note If a check valve is not working properly, replace it as described in

“Replacing the Check Valves” on page 80.
c. If the check valve assembly is functioning properly, go to step 4.

6 Troubleshooting
4. Check whether the pump can draw solvent through the tubing that connects the pressure
sensor to the rotary valve as follows:
a. Using a 1/4 in. open-ended wrench, disconnect the solvent line from the rotary valve
(see Figure 211).
• For pumps A or B, disconnect the solvent line from port 1 of the valve.
• For pump S, disconnect the solvent line from port 6 of the valve.
Figure 211. Rotary valve layout for the EASY-nLC 1000 instrument
Port 1 of valve A
Port 6 of valve S Port 1 of valve B
b. Place the free end of the solvent line into a small vial that contains the appropriate
solvent. Use solvent A for pump A and solvent B for pump B.
c. Run the Purge Solvent script and check that solvent is being aspirated from the vial
into the pump.
For information about the Purge Solvent script, see “Prepare – Purge Solvent” on
page 32.
d. Depending on whether the pump aspirated the solvent, do one of the following:
• If the pump does not aspirate solvent from the vial, go to step 5.
• If the pump aspirates solvent from the vial, the problem is probably resolved. To
verify that the system is working, go to step 4e.
e. Reconnect all of the solvent lines, and then run the Flush Air script again.
f. Depending on the results of the Flush Air script, do one of the following:
• If the Flush Air script fails, go to step 6 on page 214.
• If the Flush Air script passes, you have completed this troubleshooting procedure.

6 Troubleshooting
5. Check whether the tubing that connects the pressure sensor to the valve is blocked as
follows:
a. Reconnect the solvent line to port 1 of the valve.
b. Using a 1/4 in. open-ended wrench, disconnect the fitting connected to the top of
the pressure sensor.
c. Pipette solvent into the port on the top of the pressure sensor.
CAUTION Be careful not to spill solvent on the PCBs.

• For the PLU pump in either the EASY-nLC 1000 or EASY-nLC II
instrument, the LED panel cover for each pump protects the PCB from
accidental contact when the instrument’s right side panel is removed.
However, the cover does not form a waterproof seal with the pump body so
that the PCBs are exposed to solvent leaks from above.
• For the PLF pump in the EASY-nLC II instrument, the PCBs are completely
exposed.
d. Run the Purge Solvent script and check that the pump is aspirating solvent through
the pressure sensor.
e. Depending on whether solvent is aspirated, do one of the following:
• If the pump does not aspirate solvent, go to step 6.
• If the pump aspirates solvent, the tubing that connected the pressure sensor to
the valve is damaged. Do the following:
i. Using a 1/4 in. open-ended wrench, disconnect this tubing from the valve,
and install a new solvent line.
ii. To confirm that installing new tubing fixes the problem, run two iterations
of the Purge Solvent script. Then, run the Flush Air script with a threshold
of 10 μL for the PLF pump or 12 μL for the PLU pump.
6. To determine if the problem is in the pump, do the following:

a. Reconnect the solvent line to the top of the pressure sensor and tighten the fitting.
b. Disconnect the solvent line from the pump head by doing one of the following:
• If a PEEK fitting is connected to the pump head, use a 13 mm open-ended
wrench, to disconnect it.
• If a stainless steel fitting is connected to the pump head, use a 1/4 in. open-ended
wrench to disconnect it.
c. Pipette the appropriate solvent into the port in the pump head (see Figure 65 on
page 71).

6 Troubleshooting
d. Run the Purge script and check that the pump is aspirating solvent from the pump
head into the pump.
• If the pump does not aspirate solvent from the pump head, the problem is in the
pump.
• If the pump does aspirate solvent from the pump head, replace the tubing that
connects the pump to its pressure sensor.
7. If the problem is in the pump, verify that the piston is not dirty, broken, or scratched and
replace the piston seal as described in “Maintaining the Syringe Pumps” on page 60.

6 Troubleshooting
Troubleshooting a Pump that Fails the Leaks Script

Follow this procedure to determine why the pump failed the Leaks script.
Note For information about running the Leaks script see “Test – Leaks” on page 44.
In the Value column on the Parameters page of the Leaks script, select A to test pump A
or B to test pump B.
This procedure systematically checks whether the following problems caused the Leaks script
failure:
• Excess air in the system
• Tubing connections between the pump and the pressure sensor
• Tubing connections between pressure sensor and the valve
• A worn piston seal (in the pump head)
• A worn rotor seal (in the subsystem valve)
 To troubleshoot a pump that has failed the Leaks script
1. Run the Flush Air script for the failed pump (see “Prepare – Flush Air” on page 33).
Enter the following value for the Flush Volume parameter:
• For the PLF model pump, enter 10 μL.
• For the PLU model pump, enter 12 μL.
• If the Output page reports one of these messages, go to “Troubleshooting a Pump
that Fails the Flush Air Script” on page 212.
– Aborting unable to build pressure
– Aborting check solvent level
• If the script passes, go to step 3.
3. Run the Leaks script for the failed pump or both pumps (see “Test – Leaks” on page 44).
• If the Leaks script fails, the leak is either in the pump, the valve, or the connecting
lines or fittings. Go to step 4.
• If the Leaks script passes, excess air in the system was the source of the problem.

6 Troubleshooting
4. To determine whether the leak is between the pressure sensor and the valve or the pressure
sensor and the pump, do the following:
a. Remove the fitting from the top of the relevant pressure sensor, and replace it with a
blanking nut. Tighten the nut with a 1/4 in. open-ended wrench.
• EASY-nLC II blanking nut: LC223
• EASY-nLC 1000 blanking nut: LC523
b. Repeat the Test – Leaks script.
c. Depending on the result of the Test – Leaks script, do one of the following:
• If the Test – Leaks script passes, go to step 5, as the piston seal is leak tight and
the leak is between the pressure sensor and the valve.
• If the Test – Leaks script fails, go to step 6, as the leak is between the pressure
sensor and the pump.
5. To locate a leak between the pressure sensor and the valve, do the following:
a. Remove the blanking nut and replace the original fitting.
b. Manually check the fittings between the pressure sensor and the valve, and confirm
that they are leak tight.
If the fittings are leak tight, the valve might be the source of the leak.
c. If the valve is leaking, replace the worn rotor seal and clean or replace the stator in the
affected valve (see “Maintaining the Rotary Valves” on page 74).
d. Run the Test – Leaks script for the relevant pump and confirm that you have fixed
the leak.
6. To locate a leak between the pressure sensor and the pump, do the following:
a. Remove the blanking nut and replace the original fitting.
b. Confirm that the fittings between pump and the pressure sensor are leak tight.
c. Repeat the Test – Leaks script.
d. If the script fails again, the cause might be a worn piston seal.
e. If you suspect that the leak is caused by a worn piston seal, go to “Maintaining the
Syringe Pumps” on page 60.

6 Troubleshooting
Running a System Leak Test

To identify and locate a leak downstream from valves A and B, run the system leak test
(Test – Leaks script with System selected), and then take appropriate action as described in
Table 24 on page 221.
Table 23 lists the materials required to identify and locate leaks. Because this troubleshooting
procedure requires you to handle the solvent lines, you must wear gloves and safety glasses.
Table 23. Materials required for running the system leak test and troubleshooting leaks
Instrument Union Plug or blind fitting
EASY-nLC II P/N SC600
Zero-dead-volume
union for
1/32 in. OD tubing
EASY-nLC 1000 P/N SC900 Thermo Scientific Dionex™
P/N 6040.2303
HPLC
zero-dead-volume
union for
1/16 in. OD tubing
To run a system leak test, follow these steps:

1. “To prepare the instrument for a system leak test” on page 219
2. “To run a system leak test” on page 219

6 Troubleshooting
 To prepare the instrument for a system leak test
1. Run the Flush Air script for pump A as follows:

b. In the Category list, select Prepare. In the Name list, select Flush Air.
c. Press the Parameters tab.
d. In the Flush Threshold [μL] box, enter the following value:
• For the PLF model pump (EASY-nLC II instrument), enter 10.
• For the PLU model pump (EASY-nLC 1000 instrument), enter 12.
Figure 25 on page 33 shows the parameters for the Flush Air script.
e. Press Start.
The script starts and the Output page opens.
2. Depending on the results of the Flush Air script displayed on the Output page, do the
following:
• If the script passes, run a system leak test as described in “To run a system leak test”
on page 219.
• If one of these messages appears, go to “Troubleshooting a Pump that Fails the Flush
Air Script” on page 212.
– Aborting unable to build pressure

– Aborting check solvent level
CAUTION Wear powder-free gloves and safety glasses when handling parts of the LC
system that come into contact with solvents.
 To run a system leak test
1. If you have not already done so, run the Flush Air script to prepare the instrument for a
system leak test (see “To prepare the instrument for a system leak test” on page 219).
2. Connect the Column Out and Waste In lines with the appropriate union (see Table 23 on
page 218).
For the EASY-nLC 1000 instrument, connect these lines to the union as follows:
a. Insert the nanoViper fittings on the ends of the Column Out and Waste In lines into
the stainless steel union, and then slowly tighten the fittings until you feel resistance.

6 Troubleshooting
b. Tighten both fittings by an additional 45 degrees (1/8-turn). Do not tighten the

fittings by more than a 1/4-turn (see “Using nanoViper Fittings” on page 83).
CAUTION Because the fittings seal against each other inside the union, do not
tighten them by more than 90 degrees (1/4-turn). Overtightening the fittings can
irreparably damage their sealing surfaces.
Figure 212 shows the connection between the Column Out and Waste In lines for the
Figure 212. Column Out line connected to the Waste In line (EASY-nLC 1000 instrument)
nanoViper Union
fitting (P/N SC900)
IMPORTANT Follow the instructions in “Using nanoViper Fittings” on page 83 to

ensure that the nanoViper fittings are securely connected to the union.
3. Open the Test – Leaks script as follows:

c. In the Name list, select Leaks.
4. Set the parameters for the system leak test as follows:
b. In the Value list, select System.
5. Press Start.
The script starts and the Output page opens. During the duration of this script, the
EASY–nLC instrument pressurizes the flow paths highlighted with a dotted red line in
Figure 35 on page 45, and it monitors the flow sensors and pump piston movements to
identify and localize leaks. When the script ends, the Output page displays a message.
6. Depending on the message displayed on the Output page of the Test – Leaks script, take
the appropriate action as listed in Table 24.

6 Troubleshooting
Troubleshooting the Results of the System Leak Test

Table 24 lists the actions required to troubleshoot the results of a system leak test.
Tip The “Using nanoViper Fittings Quick Reference Guide” on page 323 describes how
to return the solvent lines in the flow path of the EASY-nLC 1000 instrument to
atmospheric pressure. Print this reference guide to refer to while troubleshooting leaks
coming from the nanoViper tubing connections.
Table 24. Output messages for a system leak test and actions to take when this test fails
Message Action
System tight. No action is required; however, the system leak test
(Sensor A <100nl/min) does not test for a a leak in valve B or pump B.
Flow sensor A should be calibrated. Rerun the system leak test. If the same message
The 0 nL/min point is off by more appears, run the Flow Sensor script to calibrate flow
than ±30 nL/min, so the software sensor A (see “Calibrate – Flow Sensors” on page 51).
cannot determine leaks.
Flow sensor B should be calibrated. Rerun the system leak test. If the same message
The 0 nL/min point is off by more appears, run the Flow Sensor script to calibrate flow
than ±30 nL/min, so the software sensor B (see “Calibrate – Flow Sensors” on page 51).
cannot determine leaks.
Check valve S for leaks. (Flow Go to “Checking Valve S for a Leak” on page 222.
sensor A >100 nL/min)
Check the sample loop for leaks. Go to “Checking the Sample Loop Connections for a
Leak” on page 222.
Check the B solvent line (valve to Go to “Locating a Leak in the Solvent Path from
flow sensor) and valve B for leaks. Valve B to Flow Sensor B” on page 223.
(Flow sensor B ±30 nL/min)
Check from pump A to Go to “Locating a Leak in the Solvent Path from
flow sensor A for leaks. (Pump A Pump A to Flow Sensor A” on page 224.
flow loss >1000 nL/min)
Check from valve S to valve W, Go to “Locating a Leak In or Between Valve S and
including valve W, for leaks. Valve W” on page 226.
Check solvent lines between Go to “Locating a Leak Between the Flow Sensors
flow sensor A and valve S, and Valve S” on page 234.
including the mixing Tee and
flow sensor B, for leaks.

6 Troubleshooting
Checking Valve S for a Leak

The system leak test returned the following message (see Table 24 on page 221):
Check valve S for leaks. (Flow sensor A >100 nL/min)
The most likely cause of this test result is a leak in the flow path between ports 3 and 4 of
valve S.
 To fix the leaking valve
1. Clean the rotor seal and stator in valve S with methanol and a lint-free swab
(see “Cleaning the Rotor Seal and Stator” on page 74).
2. Repeat the system leak test script and if it fails again, replace the rotor seal in valve S
(see “Replacing the Rotor Seal” on page 77).
3. To return the EASY-nLC instrument to normal operation as part of an LC/MS system,
secure the right side panel, reconnect the Column Out line to the column assembly, and
then reconnect the Waste In line to the venting Tee.
Checking the Sample Loop Connections for a Leak

The system leak test returned the following message (see Table 24):
Check the sample loop for leaks.
The sample loop connections are leaking, or the rotor seal in valve S is worn.
 To fix the leaking sample loop connections or the leaking valve

• For an EASY-nLC II instrument, use a 1/4 in. open-ended wrench to tighten the
sample loop fittings connected to ports 2 and 5 on valve S.
• For an EASY-nLC 1000 instrument, return the instrument to atmospheric pressure as
described in the “Using nanoViper Fittings Quick Reference Guide” on page 323.
Then individually disconnect and reconnect the nanoViper fittings connected to
ports 2 and 5 on valve S. Take care not to overtighten these fingertight fittings.
2. Rerun the system leak test (see “Running a System Leak Test” on page 218).
3. If the script still fails, clean the rotor seal and stator using methanol and a lint-free swab.
Then rerun the system leak test as described in “Cleaning the Rotor Seal and Stator” on
page 74).
4. If the problem persists, replace the rotor seal (see “Replacing the Rotor Seal” on page 77).
5. If the problem persists after replacing the rotor seal, replace the sample loop
(see “Replacing the Sample Loop” on page 89).

6 Troubleshooting
Locating a Leak in the Solvent Path from Valve B to Flow Sensor B

Check the B solvent line (valve B to flow sensor B) and valve B for leaks.
Flow sensor B has detected solvent flow toward valve B. This negative flow rate is caused by a
leak in valve B, or in the connections to port 6 of valve B and the flow sensor inlet.
Note When the system is leak tight and valve B is in the Center position, the solvent
flow through flow sensor B from pump A should be negligible. A negative flow rate of
up to –30 nL/min is within the normal range. A higher negative flow rate indicates a leak
that could affect the retention time of analytes.
Figure 213 shows a reading for flow sensor B of –60 nL/min. This means there is a leak in the
solvent path from valve B to flow sensor B.
Figure 213. Solvent line between valve B and flow sensor B
Possible leaking connections

Valve B
–60 nL/min
2
1
6 ↓
Flow sensor B
3 4 5
 To troubleshoot a leak in the solvent line connections between valve B and

flow sensor B
• For the EASY-nLC II instrument, do the following:
– Using a 1/4 in. open-ended wrench, tighten the stainless steel fitting connected
to port 6 of valve B.
– Hand tighten the PEEK fitting connected to the flow sensor inlet.
• For the EASY-nLC 1000 instrument, return the solvent system upstream of valve S to
atmospheric pressure as described in the “Using nanoViper Fittings Quick Reference
Guide” on page 323. Then individually disconnect and reconnect the nanoViper
fittings connected to port 6 on valve B and the flow sensor B inlet. Take care not to
overtighten these fingertight fittings.

6 Troubleshooting
2. Rerun the system leak test.

• If the system leak test still fails, go to “To troubleshoot a leak in valve B.”
• If the system leak test passes, return the system to normal operation.
 To troubleshoot a leak in valve B
1. Clean the rotor and stator in valve B as described in “Cleaning the Rotor Seal and Stator”
on page 74.
2. If necessary, replace the rotor seal as described in “Replacing the Rotor Seal” on page 77.
Locating a Leak in the Solvent Path from Pump A to Flow Sensor A

Check from pump A to flow sensor A for leaks. (Pump A flow loss >1000 nL/min).
The cause of this test result is a leak between flow sensor A and the inside of pump A. The
system leak test script has detected that the piston movement is 1000 nL/min more than the
flow measured at flow sensor A.
This procedure checks whether the leak is in the solvent path between the valve and the flow
sensor. If the leak in not between the valve and the flow sensor, this procedure directs you to
the “Troubleshooting a Pump that Fails the Leaks Script” on page 216 where you determine if
the leak is coming from the solvent path between the pump and the valve or from the pump
itself.
Figure 214 shows the solvent path from pump A to flow sensor A.
Figure 214. Solvent path from pump A to flow sensor A
Pump to pressure sensor Pressure sensor to valve A
Pump A Valve to flow sensor
Valve A
↓
1
2 6
Flow sensor A
3 4 5

6 Troubleshooting
 To identify a leak in pump A or the solvent path between pump A and flow sensor A
1. Run the Leaks script for pump A only as follows:

a. Set the parameters for the Leaks script as follows:
i. If you exited the Leaks script on the Maintenance > Scripts page, reopen it.
ii. Press the Parameters tab.
iii. In the Value list, select A (pump A).
b. Press Start.
2. Depending on whether the leak test for pump A passes or fails, do the following:
• If the script passes, the leak is in the solvent path from valve A to flow sensor A.
Go to step 3.
• If the script fails, the leak is in pump A. Go to “Troubleshooting a Pump that Fails
the Leaks Script” on page 216.
3. Check the connections to port 6 of valve A and the inlet to flow sensor A as follows:
• For the EASY-nLC II instrument, do the following:
– Hand tighten the PEEK fitting connected to the flow sensor inlet.
– Using a 1/4 in. open-ended wrench, tighten the stainless steel fitting connected
to port 6 of valve A.
• For the EASY-nLC 1000 instrument, return the flow path upstream of valve S to
atmospheric pressure as described in the “Using nanoViper Fittings Quick Reference
Guide” on page 323. Then individually disconnect and reconnect the nanoViper
fittings connected to port 6 on valve A and the flow sensor A inlet. Take care not to
overtighten these fingertight fittings.
4. Rerun the system leak test. Depending on whether the test fails or passes, do the
following:
• If the test fails, follow the instructions in “Maintaining the Rotary Valves” on page 74
to fix a leaking valve, which in this case is valve A. These instructions guide you
through the process of cleaning the valve’s rotor seal and stator, rerunning the system
leak test, and then replacing the rotor seal if necessary.
• If the test passes, the system is leak tight. You have completed this troubleshooting
procedure. Return the EASY-nLC instrument to normal operation.

6 Troubleshooting
Locating a Leak In or Between Valve S and Valve W

If the system leak test returns the following message (see Table 24 on page 221), follow the
workflow in Figure 215 and Figure 216 or the procedure on pages 228–234 to locate and
remedy the leak.
Check from valve S to valve W, including valve W, for leaks.
Figure 215. Workflow for locating leaks in the solvent path between valves S and W or in these valves (Part 1)
System leak test fails and returns the following message:

Check from valve S to valve W, including valve W, for leaks.
For the EASY-nLC 1000, redo the nanoViper fitting connections to the leak test union (step 1a on page 228).
For the EASY-nLC II, hand tighten the fittings connected to the leak test union.
Start the Analytical Column Equilibration script (step 1b on page 228).
No Readback
Done for flow sensor A
> 100 nL/min
Yes
Using a 1/4 in. wrench, tighten the blind, stainless steel fitting in port 1 of valve W (step 2a on page 230).
No Readback
> 100 nL/min
Yes
Set valve W to the Center position (step 3a on page 238).
No Readback
Service valve W (page 74).
for flow sensor A
Then, rerun the system leak test (page 218).
> 100 nL/min
Yes
Go to Figure 216
on the next page.

6 Troubleshooting
Figure 216. Workflow for locating leaks in the solvent path between valves S and W or in these valves (Part 2)
Continued from
Figure 215.
For the EASY-nLC 1000, redo the nanoViper connection to port 2 of valve W (step 4a on page 230).
No
For the EASY-nLC II, use a 1/4 in. open-ended wrench to tighten the stainless steel fitting in port 2 of valve W.
No Readback
> 100 nL/min
Yes
Disconnect the Waste In line from the leak test union (step 5a on page 231).
Then, block the free end of the union with a blind fitting.
No Readback
Install a new Waste In line.
for flow sensor A
> 100 nL/min
Yes
For the EASY-nLC 1000, redo the nanoViper connection to port 3 of valve S (step 6a on page 232).
For the EASY-nLC II, use a 1/4 in. open-ended wrench tighten the stainless steel fitting in port 3 of valve S.
Reconnect the solvent lines and rerun the No Readback

system leak test to confirm that the system for flow sensor A
is leak tight (page 218). > 100 nL/min
Yes
Disconnect the Column Out line from port 3 of valve S (step 7a on page 233).
Then, block port 3 of valve S with a blind fitting.
No Readback
Install a new Column Out line.
for flow sensor A
> 100 nL/min
Yes
Service valve S (page 74).

Then, rerun the system leak test.

6 Troubleshooting
Figure 217 shows the path between valves S and W for the EASY-nLC 1000 instrument.
Figure 217. Solvent path between valve S and valve W
Valve S Valve W
Blind fitting
connected
Column Out Waste In to port 1
line line
Leak test
union
 To locate and remedy a leak in valve S or valve W or in the solvent path between
these valves
1. Make sure that the connections to the leak test union are secure as follows:
a. Depending on the instrument model, do the following:
• For the EASY-nLC II instrument, hand tighten the PEEK fittings.
i. Disconnect the nanoViper fittings from the union.

ii. Reinsert the nanoViper fittings into the stainless steel union. Then, slowly
tighten the fittings until you feel resistance.
iii. Tighten both fittings by an additional 45 degrees (1/8-turn). Do not
tighten the fittings by more than 90 degrees (1/4-turn).
For more information, see “Using nanoViper Fittings” on page 83.
.
Note The connections to the leak test union are one of the most common sources
of leaks for the system leak test.
b. For leak testing, set up and start the Analytical Column Equilibration script as
follows:
i. On the Maintenance > Scripts page, select Prepare in the Category list, and then
select Analytical Col Equilibration in the Name list.
ii. Press the Parameters tab.
iii. In the Volume [μL] box, enter 140. This volume should be sufficient to keep the
solvent flow on during this troubleshooting procedure.
iv. Leave the Flow box [μL/min] box empty so that pump A operates at the set
pressure.

6 Troubleshooting
v. In the Max Pressure [bar] box, enter 280 bar for the EASY-nLC II instrument
or 980 bar for the EASY-nLC 1000 instrument.
vi. Press Start.
The instrument places the valves in the following positions, and pump A begins
pumping solvent through flow sensor A.
• Valve A: 1–6 • Valve S: 1–2

• Valve B: Center • Valve W: 1–2
Figure 218 shows the solvent system schematic on the Home > Overview page. Use
this page to monitor the readback for flow sensor A and to access the valve controls.
For information about changing the valve positions, see “Using the Valve Controls”
on page 204.
Figure 218. Home > Overview page showing the readback for flow sensor A
Readback Press this icon to
for flow sensor A with open the controls
a flow < 100 nL/min for valve W.
c. On the Home > Overview page, check the readback for flow sensor A. Then,
depending on the flow rate, do one of the following:
• If the flow rate is <100 nL/min, you have remedied the leak and completed this
troubleshooting procedure. Return the instrument to normal operation.
• If the flow rate is >100 nL/min, go to the next step.

6 Troubleshooting
2. Make sure that the connection between the blind fitting and port 1 of valve W is leak
tight as follows:
a. Using a 1/4 in. open-ended wrench, tighten the stainless steel blind fitting connected
to port 1 of valve W.
b. With the Analytical Column Equilibration script running, monitor flow sensor A.
Then, depending on the flow rate, do one of the following:
• If the flow is <100 nL/min, you have remedied the leak and completed this
• If the flow is >100 nL/min, go to the next step.
3. Check if valve W is leaking as follows:
a. On the Home > Overview page, press the valve W icon and set the valve to the
Center position.
Placing valve W in the Center position blocks the solvent flow into valve W and
eliminates valve W as the possible source of the leak.
Depending on the flow rate, do one of the following:
• If the flow is <100 nL/min with valve W removed from the solvent path, valve W
is the source of the system leak. To fix the leaking valve, follow the instructions in
“Maintaining the Rotary Valves” on page 74 to clean the valve, replace the rotor,
and if necessary, replace the stator. Then, rerun the system leak test.
4. Check for a leak-tight connection to port 2 of valve W as follows:
fitting to port 2 of valve W.
i. On the Home > Overview page, change the position of the following
valves to return the system to atmospheric pressure:
– Valve S: Center
– Valve W: 1–6
ii. Disconnect and then reconnect the nanoViper fitting from port 2 of
valve W. Take care to avoid overtightening the fingertight fitting.
iii. On the Home > Overview page, reset valves A and S as follows:
– Valve S: 1–2
– Valve W: 1–2

6 Troubleshooting
• If the flow is <100 nL/min, you have remedied the leak and completed this
5. Check the Waste In line as follows:
• For the EASY-nLC II instrument, disconnect the Waste In line from the leak test
union. Then, block the free end of the union with a blind fitting.
i. On the Home > Overview page, change the position of the following
valves to return the system to atmospheric pressure:
– Valve S: Center
– Valve W: 1–6
ii. Using the black knurled nut to loosen the nanoViper fitting, disconnect
the Waste In line from the leak test union. Then, block the free end of the
union with a blind fitting.
iii. On the Home > Overview page, reset valves S and W as follows:
– Valve S: 1–2
– Valve W: 1–2
Figure 219 shows the Waste In line disconnected from the leak test union and the
free end of the union plugged with a blind fitting.

6 Troubleshooting
Figure 219. Setup for eliminating the Waste In line as the source of the system leak
Blind fitting
Valve S Valve W
From the
mixing Tee
• If the flow is <100 nL/min, install a new Waste In line. Then, reconnect the
solvent lines and rerun the system leak test as described in “Running a System
Leak Test” on page 218.
For ordering information, see Appendix C, “Consumables and Replacement
Parts.”
6. Check for a leak-tight connection to port 3 of valve S as follows:
fitting to port 3 of valve S.
i. On the Home > Overview page, set valve S to the Center position to
return the system to atmospheric pressure:
ii. Disconnect and then reconnect the Column Out line to port 3 of valve S.
Take care to avoid overtightening the fingertight fitting.
iii. On the Home > Overview page, reset valve S to position 1–2.

6 Troubleshooting
• If the flow is <100 nL/min, reconnect the solvent lines and rerun the system leak
test as described in “Running a System Leak Test” on page 218 to confirm that
the system is leak tight.
7. Determine whether the leak is in the Column Out line or in valve S as follows:
• For the EASY-nLC II instrument, use a 1/4 in. open-ended wrench to disconnect
the Column Out line from port 3 of valve S. Plug the port with a blind fitting.
Then, use a 1/4 in. open-ended wrench to tighten the fitting.
i. On the Home > Overview page, set valve S to the Center position to
ii. Using the black knurled nut, disconnect the Column Out line from port 3
of valve S. Then, block port 3 of valve S with a blind fitting.
iii. On the Home > Overview page, reset valve S to position 1–2.
Figure 220 shows port 3 of valve S plugged with a blind fitting.

Figure 220. Port 3 of valve S plugged with a blind fitting
Valve S Valve W
From the
mixing Tee
Blind fitting
in port 3 of valve S

6 Troubleshooting
• If the flow is <100 nL/min, install a new Column Out line. Then, reconnect the
solvent lines and rerun the system leak test as described in “Running a System
Leak Test” on page 218.
For ordering information, see Appendix C, “Consumables and Replacement
Parts.”
• If the flow is >100 nL/min, remedy the leak in valve S as described in
“Maintaining the Rotary Valves” on page 74. Then, rerun the system leak test as
described in “Running a System Leak Test” on page 218.
Locating a Leak Between the Flow Sensors and Valve S

When one or more of the connections are leaking in the solvent path between the flow sensor
outlets and the mixing Tee inlets, the system leak test returns this message (see Table 24 on
page 221:
Check solvent lines between flow sensor A and valve S, including the mixing Tee and
flow sensor B, for leaks.
As the flow sensors and mixing Tee differ for the EASY-nLC 1000 and EASY-nLC II
instruments, follow the topic for your instrument to locate and remedy the leak:
• “EASY-nLC 1000: Locating a Leak Between the Flow Sensors and Valve S,” on
pages 235–245
• “EASY-nLC II: Locating a Leak Between the Flow Sensors and Valve S” on page 246

6 Troubleshooting
EASY-nLC 1000: Locating a Leak Between the Flow Sensors and Valve S
To determine whether the leak is coming from the connection to port 4 of valve S,
the connection to the mixing Tee outlet, or the connections between the flow sensor
outlets and the mixing Tee inlets, follow the workflow in Figure 221 or the procedure on
pages 236–239.
Figure 221. EASY-nLC 1000 workflow for locating leaks between the flow sensors and valve S
System leak test fails and returns the following message:
Check solvent lines between flow sensor A and valve S, including the mixing Tee and flow sensor B, for leaks.
Redo the nanoViper fitting connection to port 4 of valve S (step 1a on page 236).
Start the Analytical Column Equilibration script (step 1b on page 236).
No Readback
> 100 nL/min
Yes
Disconnect the nanoViper fitting from the mixing Tee outlet.
Then, block the mixing Tee outlet with a blind fitting (step 2 on page 236).
Install a new solvent line

between port 4 of valve S
and the mixing Tee outlet No Readback
(step 2d on page 238). for flow sensor A
> 100 nL/min
Then, reconnect the plumbing and
rerun the system leak test (page 218).
Yes
Disconnect the blind fitting from the mixing Tee outlet, and then reconnect the
solvent line to the mixing Tee outlet. Disconnect the solvent line from the mixing
Tee inlet for the solvent B channel, and then block the inlet with a blind fitting
(step 3 on page 238).
No Readback Yes
for flow sensor A
> 100 nL/min
Go to “EASY-nLC 1000: Locating a Leak Between Go to “EASY-nLC 1000: Locating a Leak Between
Flow Sensor A and the Mixing Tee” on page 240. Flow Sensor B and the Mixing Tee” on page 243.

6 Troubleshooting
 To locate leaks between the flow sensors and valve S in the EASY-nLC 1000
instrument
1. To ensure a leak-tight connection to port 4 of valve S, do the following:
a. Disconnect and then reconnect the nanoViper fitting to port 4 of valve S.
b. From the Maintenance > Scripts page, start the Analytical Column Equilibration
script with the maximum pressure set to 980 bar and the volume set to 140 μL.
For information about setting up the Analytical Column Equilibration script, see
step 1b on page 228.
When you start the Analytical Column Equilibration script, the instrument sets the
rotary valves to these positions and begins pumping solvent through flow sensor A:
• Valve A: 1–6
• Valve B: Center
• Valve S: 1–2
• Valve W: 1–2
2. To check the solvent line that connects the mixing Tee outlet to port 4 of valve S, do the
following:
a. On the Home > Overview page, set valves A and W to the following positions to
• Valve A: Center
• Valve W: 1–6
For information about changing the valve positions, see “Using the Valve Controls”
on page 204.
b. Disconnect the nanoViper fitting from the mixing Tee outlet.Then, block the mixing
Tee outlet with a blind fitting (see Figure 222).

6 Troubleshooting
Figure 222. Mixing Tee outlet plugged with a blind fitting

Waste In line
Leak
test
union
Column Out line

Solvent line that connects the
mixing Tee outlet to port 4 of valve S
Inline filter
connected to the Blind fitting connected to the mixing Tee outlet
outlet of
flow sensor A
Inline filter
connected to the
outlet of
flow sensor B
c. On the Home > Overview page, reset these valve positions:

• Valve A: 1–6
• Valve W: 1–2

6 Troubleshooting
d. On the Home > Overview page, check the readback for flow sensor A. Then,
• If the flow rate is <100 nL/min, do the following:
i. Stop the Analytical Column Equilibration script and return the system to
atmospheric pressure.
ii. Disconnect the damaged solvent line from port 4 of valve S.
iii. Install a new solvent line to connect the mixing Tee outlet to port 4 of
valve S.
For ordering information, see Table 33 on page 316.
iv. Rerun the system leak test (see “Running a System Leak Test” on
page 218).

3. To eliminate the solvent B channel as the leak source, do the following:
a. Set valve A to the Center position to return the system to atmospheric pressure while
maintaining pressure on the front end of the system.
b. Disconnect the blind fitting from the mixing Tee outlet, and then reconnect the
solvent line to the mixing Tee outlet.
c. Disconnect the solvent line from the mixing Tee inlet for the solvent B channel, and
then block the inlet with a blind fitting.
Figure 223 shows the solvent line disconnected from the mixing Tee and a blind
fitting in the inlet port of the mixing Tee for the solvent B channel.
d. Reset valve A to position 1–6.

6 Troubleshooting
Figure 223. Mixing Tee inlet for the solvent B channel plugged with a blind fitting
Leak
test
union
Solvent line that connects the

mixing Tee outlet to port 4 of valve S
Mixing Tee inlet for the solvent B channel

plugged with a blind fitting
e. On the Home > Overview page, check the readback for flow sensor A. Then,
• If the flow rate is <100 nL/min, go to “EASY-nLC 1000: Locating a Leak
Between Flow Sensor B and the Mixing Tee” on page 243, as removing the
solvent B channel from the flow path remedied the leak.
• If the flow rate is >100 nL/min, the leak is in the solvent A channel, as removing
the solvent B channel from the solvent path did not remedy the leak. Go to the
next procedure, “EASY-nLC 1000: Locating a Leak Between Flow Sensor A and
the Mixing Tee.”

6 Troubleshooting
EASY-nLC 1000: Locating a Leak Between Flow Sensor A and the Mixing Tee
By following the workflow in Figure 221 on page 235 or the procedure on pages 236–239,
you determined that the leaking connection is between flow sensor A and the mixing Tee. The
system plumbing is set up as shown in Figure 223 on page 239, with the solvent channel B
disconnected from the mixing Tee.
Follow the workflow in Figure 224 or the procedure on pages 241– 242 to locate and remedy
the leak.
Figure 224. EASY-nLC 1000 workflow for locating a leak between flow sensor A and the mixing Tee (Part 1)
You determined that the leak is in the solvent path

between the outlet of flow sensor A and the mixing Tee inlet.
Disconnect the solvent line from the outlet of flow sensor A.

Then, block the outlet with a blind fitting (step 1b on page 241).
Install a new solvent line between the

flow sensor A outlet and the mixing Tee No Readback
inlet (step 1d on page 242). for flow sensor A
Then, reconnect all of the solvent lines and > 100 nL/min
Yes
Using a 5/16 in. open-ended wrench, tighten the inline filter

to the outlet of flow sensor A (step 2a on page 242).
Readback
Reconnect all of the solvent lines, and No
for flow sensor A
then rerun the system leak test (page 218).
> 100 nL/min
Yes
Replace the inline filter (page 81). Then,

reconnect all of the solvent lines and

6 Troubleshooting
 To locate and remedy a leak between flow sensor A and the mixing Tee in the
EASY-nLC 1000
1. To check if you must replace the solvent line that connects the outlet of flow sensor A to
the mixing Tee, do the following:
a. Set valve A to the Center position.
b. Disconnect the solvent line from the inline filter that connects to the outlet of
flow sensor A. Then, block the inline filter with a blind fitting.
Figure 225 shows the solvent path blocked at the outlet of flow sensor A.
c. Reset valve A to position 1–6.
Figure 225. Solvent A channel blocked at the outlet of flow sensor A
If the flow is <100 nL/min

with this line removed
from the solvent path,
install a new solvent line.
Outlet of flow sensor A

plugged with a blind fitting

6 Troubleshooting
d. Check the readback for flow sensor A. Then, depending on the flow rate, do one of
the following:
i. Stop the Analytical Column Equilibration script.

ii. Disconnect the damaged solvent line from the mixing Tee’s inlet for the
solvent A channel.
iii. Install a new solvent line between the mixing Tee’s inlet for the solvent A
channel and the flow sensor’s outlet.
iv. Reconnect the solvent lines and rerun the system leak test (see “Running a
System Leak Test” on page 218).

2. To check the connection between the inline filter and the flow sensor A outlet, do the
following:
a. Using a 5/16 in. open-ended wrench, tighten the inline filter to the outlet of
flow sensor A.
b. Check the readback for flow sensor A. Then, depending on the flow rate, do one of
the following:

ii. Reconnect all of the solvent lines.
iii. Rerun the system leak test (see “Running a System Leak Test” on
page 218).
• If the flow rate is >100 nL/min, do the following:

ii. Remove the damaged inline filter and install a new inline filter.
page 218).

6 Troubleshooting
EASY-nLC 1000: Locating a Leak Between Flow Sensor B and the Mixing Tee
By following the workflow in Figure 221 on page 235 or the procedure on pages 236–239,
you determined that the leaking connection is between the flow sensor B outlet and the
mixing Tee inlet. The system plumbing is set up as shown in Figure 223 on page 239, with
the solvent channel B disconnected from the mixing Tee inlet.
Follow the workflow in Figure 226 or the procedure on pages 244–245 to locate and remedy
the leak.
Figure 226. EASY-nLC 1000 workflow for locating a leak between flow sensor B and the mixing Tee
You determined that the leak is in the solvent path
between the outlet of flow sensor B and the inlet of the mixing Tee.
Remove the blind fitting from the solvent B channel inlet of the mixing Tee. Reconnect the solvent line to the solvent B
channel inlet of the mixing Tee. Redo the nanoViper connection to the outlet of flow sensor B (step 1 on page 244).
The system plumbing now matches that for a system leak test (see Figure 35 on page 45).
No Readback
> 100 nL/min
Yes
Using a 5/16 in. open-ended wrench,

tighten the inline filter to the outlet of
flow sensor B (step 2 on page 244).
No Readback
> 100 nL/min
Yes
Disconnect the solvent line from the outlet of flow sensor B. Then, plug the free end of
the solvent line with a leak test union and a blind fitting (step 3 on page 244).
Install a new inline filter (page 81). No Readback

Reconnect all of the solvent lines. Then, for flow sensor A
rerun the system leak test (page 218). > 100 nL/min
Yes
Install a new solvent line between the flow sensor B outlet and the mixing Tee inlet
(step 3d on page 245). Rerun the system leak test (page 218).

6 Troubleshooting
 To locate a leak between flow sensor B and the mixing Tee in the EASY-nLC 1000
1. To ensure leak-tight connections for the solvent line that connects the outlet of flow
sensor B to the mixing Tee inlet, do the following:
b. Set up the system plumbing as follows:
i. Remove the blind fitting from the mixing Tee’s inlet for the solvent B channel.
ii. Reconnect the solvent line to the solvent B channel inlet of the mixing Tee.
iii. Redo the nanoViper connection to the mixing Tee’s inlet for the solvent B
channel.
The system plumbing now matches that for a system leak test.
the following:
• If the flow rate is <100 nL/min, you have completed this troubleshooting
procedure. Return the instrument to normal operation.
2. Using a 5/16 in. open-ended wrench, tighten the inline filter to the outlet of
flow sensor B.
3. To determine whether the solvent line or the inline filter is the leak source, do the
following:
b. Disconnect the solvent line from the outlet of flow sensor B. Then, plug the free end
of the solvent line with a leak test union and a blind fitting (see Figure 227).

6 Troubleshooting
Figure 227. Solvent line disconnected from the outlet of flow sensor B
Inlets of the EASY-nLC 1000 flow sensors
Inline filter connected to

the outlet of flow sensor B
Solvent line disconnected

from the outlet of flow sensor B
and plugged with a union and a
blind fitting
the following:

ii. Remove the damaged inline filter from the outlet of flow sensor B and
install a new inline filter.
iii. Reconnect the system plumbing and rerun the system leak test (see
“Running a System Leak Test” on page 218).
• If the flow rate is >100 nL/min, do the following:

ii. Install a new solvent line between the flow sensor B outlet and the mixing
Tee inlet.
page 218).

6 Troubleshooting
EASY-nLC II: Locating a Leak Between the Flow Sensors and Valve S
Figure 228 on page 247 shows the solvent lines that connect the flow sensor outlets to the
mixing Tee and the solvent line that connects the mixing Tee outlet to port 4 of valve S.
 To systematically locate and remedy a leak in an EASY-nLC II instrument from the

flow sensor outlets to port 4 of valve S
1. To ensure a leak-tight connection to port 4 of valve S, do the following:
a. Tighten the fitting in port 4 of valve S.
b. From the Maintenance > Scripts page, start the Analytical Column Equilibration
script with the maximum pressure set to 280 bar and the volume set to 140 μL.
For information about setting up the Analytical Column Equilibration script, see
step 1b on page 228.
2. Hand tighten the following PEEK fittings:
• Fittings connected to the mixing Tee
• Fittings connected to the flow sensor outlets
3. With the Analytical Column Equilibration script running, monitor flow sensor A.
Depending on the flow rate, do one of the following:
• If the flow is <100 nL/min, tightening the solvent line connections remedied the
leak, and you have completed this troubleshooting procedure. Return the instrument
to normal operation.
• If the flow is >100 nL/min, the leak is coming from one of the solvent lines. Go to
the next step.
Note For information about ordering solvent lines for the EASY-nLC II instrument,
see Table 32 on page 314.
4. Replace the solvent line that connects the mixing Tee outlet and port 4 of valve S. Restart
the Analytical Column Equilibration script and monitor flow sensor A.
• If the flow is <100 nL/min, you have completed this troubleshooting procedure.

6 Troubleshooting
5. Replace the solvent line that connects the outlet of flow sensor A to the mixing Tee inlet.
Restart the Analytical Column Equilibration script and monitor flow sensor A.
6. Replace the solvent line that connects the outlet of flow sensor B to the mixing Tee inlet.
Restart the Analytical Column Equilibration script and monitor flow sensor A.
• If the flow is >100 nL/min, contact your local Thermo Fisher Scientific field service
engineer.
Figure 228. Solvent lines that connect the flow sensor outlets to the mixing Tee and the solvent line that connects the mixing
Tee outlet to port 4 of valve S in the EASY-nLC II instrument
Solvent line that connects
Mixing Tee
the outlet of flow sensor A
with fingertight
to the mixing Tee
connections

the outlet of flow sensor B
to the mixing Tee
Column Out and
Waste In lines
connected to the Valve W Valve S
leak test union
1 1
6
6
2
2
5
5
3
4 4

the mixing Tee outlet
to port 4 of valve S
Flow sensor outlets

with fingertight connections
+
–
Solvent lines
that connect
valves A and B
to the flow sensor inlets

6 Troubleshooting
Identifying a Leaking Check Valve
Identifying a Leaking Check Valve

The EASY-nLC instrument has four check valves. Each solvent inlet line connects to a check
valve assembly with a solvent-side check valve and a waste-side check valve.
 To determine if the waste-side check valve is leaking
1. Run the Purge Solvent script as follows:

e. Select the check box for the appropriate pump.
f. Press Start.
2. As the pump is filling, observe the waste line.
If you observe solvent moving toward the check valve assembly, the waste-side check valve
is leaking.
3. If the waste-side check valve is leaking, replace it and repeat the Purge Solvent script.
 To determine if the solvent-side check valve is leaking
1. Start the Purge Solvent script.

2. As the pump is emptying, observe the solvent line.
If you observe solvent moving toward the solvent bottle from the check valve assembly,
the solvent-side check valve is leaking.
3. If the solvent-side check valve is leaking, replace it and repeat the Purge Solvent script.

6 Troubleshooting
Troubleshooting a System Blockage

Use this troubleshooting procedure when the back pressure for a chromatographic method
rises above the expected level or when the flow decreases below the set rate for the column
equilibration or sample loading steps.
In most cases, an increase in back pressure is caused by a blocked column or a blocked

Column Out line. The Column Out line has an ID of 30 μm for the EASY-nLC II
instrument and 20 μm for the EASY-nLC 1000 instrument and is the smallest ID line that
the sample passes through, from sample pickup to the columns.
Troubleshooting a system blockage requires these tools and materials.

1/4 in. open-ended wrench • Powder-free gloves
to loosen the stainless steel
• EASY-nLC II instrument: HPLC union, P/N SC600
fittings
• EASY-nLC 1000 instrument: HPLC union, P/N SC900
When running the Back Pressure script, the system also checks for an unusually low back
pressure. If the back pressure is unusually low, the system probably has a leak.
To troubleshoot a system blockage, follow these procedures:

1. “Running the Back Pressure Test for the A and B Solvent Paths” on page 250
2. Depending on the test results, replace the blocked components in the column assembly or
follow one or both of these procedures:
• “Troubleshooting a System Blockage when Test Solvent A Fails” on page 251
• “Troubleshooting a System Blockage when Test Solvent B Fails” on page 257

6 Troubleshooting
Running the Back Pressure Test for the A and B Solvent Paths
The Back Pressure script determines instrument back pressure for solvent lines A and B. The
script runs at a preset flow and measures the back pressure on the system.
IMPORTANT Before you perform the Back Pressure script, ensure that the solvent A
bottle contains water and the solvent B bottle contains acetonitrile. This test is not valid
for other solvents.
 To run the back pressure script for both the A and B solvent paths
1. Remove the columns and connect the Column Out line to the Waste In line using the
appropriate HPLC union.
Instrument Union
EASY-nLC II SC600
EASY-nLC 1000 SC900
2. Run the Back Pressure scripts for both Solvent A and Solvent B as follows:
c. In the Name list, select Back Pressure.
e. Select the Test Solvent A and Test Solvent B check boxes.
f. Press Start.
3. Depending on the test results, do one of the following:
• If the Test Solvent A test fails and the following message appears, go to
“Troubleshooting a System Blockage when Test Solvent A Fails” on page 251.
– EASY-nLC II instrument—Pressure is xxx bar (exceeds 100 bar limit), test failed!
– EASY-nLC 1000 instrument—Pressure is xxx bar (exceeds 175 bar limit), test
failed!
• If the Test Solvent B test fails and the following message appears, go to
“Troubleshooting a System Blockage when Test Solvent B Fails” on page 257.
Pressure is xxx bar (exceeds 100 bar limit), test failed!
• If both Test Solvent A and Test Solvent B tests pass and the following message
appears, inspect and if necessary replace the columns, the packed emitter, or both.
Pressure is xxx bar, test passed.

6 Troubleshooting
Troubleshooting a System Blockage when Test Solvent A Fails

Follow this procedure when the Back Pressure test for Test Solvent A fails (see “Running the
Back Pressure Test for the A and B Solvent Paths” on page 250).
 To verify the system blockage
1. Run the Precolumn Equilibration script and check the back pressure as follows:
a. On the Maintenance > Scripts page, select Prepare in the Category list, and then
select Precolumn Equil in the Name list.
c. In the Volume [μL] box, enter 140 μL.
d. In the Flow [μL/min] box, enter 2 μL/min.
e. Leave the Max Pressure [bar] box blank.
f. Press Start.
g. Monitor the pump A pressure trace.
2. Depending on the back pressure, do the following:
• If the back pressure is below the pressure threshold, the system blockage has been
removed. To confirm that the back pressure is below the pressure threshold, rerun the
Back Pressure script with the Test Solvent A check box selected.
• If the back pressure is above the pressure threshold, keep the Precolumn Equil script
running and go to “To locate the source of the blockage when the Test Solvent A test
fails” on page 253.
Instrument Pressure threshold

EASY-nLC II 100 bar
EASY-nLC 1000 175 bar

6 Troubleshooting
Figure 229 shows the areas that the following procedure systematically checks for blockage.
Figure 229. Solvent path from pressure sensor A to the Waste In line
1
2 6 1. Valve W
2. Waste In line 3 4 5
Note.
Disconnect the Column Out and the
Waste In lines from the union after
testing valve W for blockage.
Valve S
3. Column Out line 4. Valve S 1

2 6
3 4 5
5. Valve S (port 4)
to mixing Tee
6. Mixing Tee
7. Mixing Tee to
flow sensor A 13. Valve A (port 1) to
outlet pressure sensor
8. Inline filter Valve A

(EASY-nLC 1000 instrument) ↓ 9. Flow sensor A
10. Inline filter 1

2 6
(EASY-nLC 1000 instrument)
3 4 5
12. Valve A
11. Valve A (port 6)

to flow sensor
inlet

6 Troubleshooting
 To locate the source of the blockage when the Test Solvent A test fails
1. To determine if valve W is blocked, do the following:

a. Make sure that the Precolumn Equilibration script is set up and running as described
in step 1 on page 251 and that the Column Out and Waste In lines are connected
with a union.
b. Disconnect the Waste In line from port 2 of valve W (see Figure 229 on page 252).
c. Depending on the back pressure, do one of the following:
• If the pressure is below the threshold, valve W is blocked. Go to “Maintaining
the Rotary Valves” on page 74.
• If the pressure is above the threshold, go to step 2.
2. To determine if the Waste In line is blocked, do the following:
a. Disconnect the Column Out line and the Waste In line from the union.
Column Out line Union Waste In line
b. Depending on the back pressure, do one of the following:

• If the pressure is below the threshold, the Waste In line is blocked. Discontinue
this troubleshooting procedure and replace the Waste In line with a new line.

EASY-nLC II 100 bar
• If the pressure is above the threshold, go to step 3.

3. To determine if the Column Out line is blocked, do the following:
a. Disconnect the Column Out line from port 3 of valve S.
• If pressure is below the threshold, the Column Out line is blocked. Discontinue
this troubleshooting procedure and replace the Column Out line with a new line.

EASY-nLC II 100 bar
• If the pressure is above the threshold, reconnect the Column Out line, and then
go to step 4.

6 Troubleshooting
4. To determine if valve S is partially or totally blocked, do the following:

a. Disconnect the mixing Tee line from port 4 of valve S.
• If the pressure is below the threshold, valve S is partially or totally blocked.
Discontinue this troubleshooting procedure and go to “Maintaining the Rotary
Valves” on page 74.

EASY-nLC II 100 bar
• If the pressure is above the threshold, reconnect the mixing Tee line to port 4 of
valve S, and then go to step 5.
5. To determine if the line that connects valve S to the mixing Tee is blocked, do the
following:
a. Disconnect the line from the mixing Tee.
• If the pressure is below the threshold, the line that connects the mixing Tee to
valve S is blocked. Replace it.

EASY-nLC II 100 bar
• If the pressure is above the threshold, reconnect the line to the mixing Tee, and
then go to step 6.
6. To determine if the mixing Tee is blocked, do the following:
a. Disconnect the line that exits flow sensor A from the mixing Tee.
• If the pressure is below the threshold, the mixing Tee is blocked. Clean the
mixing Tee, or if necessary replace it.

EASY-nLC II 100 bar
• If the pressure is above the threshold, reconnect the line to the mixing Tee, and
then go to step 7.

6 Troubleshooting
7. To determine if the line that connects the mixing Tee to flow sensor A is blocked, do the
following:
a. Disconnect the line from the outlet of flow sensor A.
• If the pressure is <20 bar, the line that connects the mixing Tee to flow sensor A
is blocked. Replace it with a new solvent line.
• If the pressure is >20 bar, reconnect the line to flow sensor A, and then go to
step 8 for an EASY-nLC 1000 instrument or step 9 for an EASY-nLC II
instrument.
8. To determine if the inline filter connected to the flow sensor outlet of the
EASY-nLC 1000 system is blocked, do the following:
a. Remove the inline filter from the flow sensor outlet.
• If the pressure is <20 bar, the inline filter is blocked. Replace it with a new filter.
• If the pressure is >20 bar, reconnect the inline filter to flow sensor A, and then go
to step 9.
9. To determine if flow sensor A is blocked, do the following:
a. Disconnect the solvent line from the flow sensor A inlet.
b. Depending on the back pressure for flow sensor A, do one of the following:
• If the pressure is <20 bar, flow sensor A is blocked. Replace it with a new flow
sensor as described in “Replacing a Flow Sensor” on page 92.
• If the pressure is >20 bar, reconnect the line to flow sensor A, and then go to
step 10 for an EASY-nLC 1000 system or step 11 for an EASY-nLC II system.
10. To determine if the inline filter connected to the flow sensor inlet of the EASY-nLC 1000
system is blocked, do the following:
a. Remove the inline filter from the flow sensor inlet.
• If the pressure is <20 bar, the inline filter is blocked. Replace it with a new inline
filter.
to step 11.

6 Troubleshooting
11. To determine if the line that connects valve A to flow sensor A is blocked, do the
following:
a. Disconnect the solvent line from port 6 of valve A.
• If the pressure is <20 bar, the line from valve A to flow sensor A is blocked.
Replace it with a new solvent line.
• If the pressure is >20 bar, reconnect the line to valve A, and then go to step 12.
12. To determine if valve A is blocked, do the following:
a. Disconnect the solvent line from port 1 of valve A.
• If the pressure is <20 bar, valve A is blocked. Inspect the valve and clean the
stator. If the blockage persists, replace the rotor seal.
• If the pressure is >20 bar, reconnect the line to valve A, and then go to step 13.
13. To determine if the line from pressure sensor A to valve A is blocked or if
pressure sensor A is blocked, do the following:
a. Disconnect the solvent line from the outlet of pressure sensor A.
• If the pressure is <20 bar, the line that connects pressure sensor A to valve A is
blocked. Replace it with a new solvent line.
• If the pressure is >20 bar, pressure sensor A is blocked. Replace it with a new
pressure sensor as described in “Replacing a Pressure Sensor for the PLU Pump”
on page 90.

6 Troubleshooting
Troubleshooting a System Blockage when Test Solvent B Fails

Follow this procedure when the Back Pressure test for Test Solvent B fails (see “To run the
back pressure script for both the A and B solvent paths” on page 250).
Figure 230 shows the areas that this procedure systematically checks for blockage.
Figure 230. Solvent system from pressure sensor B to the mixing Tee
1. Mixing Tee
2. Flow sensor outlet to

the mixing Tee
3. Inline filter for the

EASY-nLC 1000 instrument
↓ 4. Flow sensor
5. Inline filter for the

EASY-nLC 1000 instrument
6. From valve B (port 6) to

the flow sensor inlet
1
2 6
7. Valve B
3 4 5
8. Valve B (port 1)
–or–
the pressure sensor

6 Troubleshooting
 To troubleshoot a system blockage when only the Test Solvent B test fails
1. To determine if the blockage is in the mixing Tee, do the following:

a. Make sure that the Column Out line is connected to the Waste In line with a union.
b. Remove the solvent line from the mixing Tee that connects it to flow sensor B.
c. Repeat the Back Pressure script with the Test Solvent B check box selected.
d. Depending on the test results, do one of the following:
• If Test solvent B passes, clean the mixing Tee and if necessary replace it.
• If Test solvent B fails, go to step 2.
2. To determine if the blockage is in the solvent line that connects the B flow path to the
mixing Tee, do the following:
a. Disconnect the solvent line from the outlet of flow sensor B.
b. Place valve B in position 1–6 as follows:
i. Press Home > Overview.
ii. Press the valve B icon.
iii. In the Valve B dialog box, press 1–6.
c. Set pump B to deliver 2 μL/min as follows:
i. Press the pump B icon.
ii. In the flow rate box, type 2 μL/min.
iii. Press Start.
iv. Leave the dialog box open.
For more information about the direct controls for the pump, see “Using the Pump
d. Monitor the Pressure readback box for pump B. Then, depending on the back
pressure, do one of the following:
• If the pressure is <20 bar, the solvent line is blocked.
– For the EASY-nLC II instrument, replace the solvent line with a new fused
silica line. Then, to confirm that the blockage was in the discarded solvent
line, repeat the Back Pressure script with the Test Solvent B check box
selected.
– For the EASY-nLC 1000 instrument, place valve B in position 1–2 to release
the pressure. Remove the blocked nanoViper line and replace it with a new
nanoViper line. Then, to confirm that the blockage was in the discarded
solvent line, repeat the Back Pressure script with the Test Solvent B check
box selected.
• If the pressure is >20 bar, keep pump B running and go to step 3 for the
EASY-nLC 1000 instrument or step 4 for the EASY-nLC II instrument.

6 Troubleshooting
3. For the EASY-nLC 1000 instrument, to determine if the inline filter connected to the
flow sensor outlet is blocked, do the following:
to step 4.
4. To determine if flow sensor B is blocked, do the following:
a. Disconnect the solvent line from the inlet of flow sensor B, and then monitor the
pressure.
b. Depending on the pressure, do one of the following:
• If the pressure is <20 bar, flow sensor B is blocked. Replace it as described in
“Replacing a Flow Sensor” on page 92.
• If the pressure is >20 bar, keep pump B running and go to step 5 for the
EASY-nLC 1000 instrument or step 6 for the EASY-nLC II instrument.
5. For the EASY-nLC 1000 instrument, to determine if the inline filter connected to the
inlet of flow sensor B is blocked, do the following:
to step 6.
6. To determine if the line that connects valve B to flow sensor B is blocked, do the
following:
a. Disconnect the line from port 6 of valve B, and then monitor the pressure.
• If the pressure is below the threshold, the solvent line is blocked. Discontinue
this troubleshooting procedure, and replace the solvent line that connects port 6
of valve B to the flow sensor inlet.

EASY-nLC II 20 bar
• If the pressure is above this threshold, keep the pump running and go to step 7.

6 Troubleshooting
7. To determine if valve B is blocked, do the following:

a. Remove the solvent line from port 1 of valve B, and then monitor the pressure.
• If the pressure is below the threshold, valve B is blocked. Go to “Maintaining the
Rotary Valves” on page 74.

EASY-nLC II 20 bar
• If the pressure is above the threshold, keep the pump running and go to step 8.
8. To determine if either the line that connects valve B to pressure sensor B is blocked or
pressure sensor B is blocked, do the following:
a. Remove the solvent line that connects valve B to pressure sensor B from
pressure sensor B, and then monitor the pressure.
• If the pressure is below the threshold, the solvent line is blocked. Replace it.
Instrument Threshold pressure

EASY-nLC II 20 bar
• If the pressure is >20 bar, pressure sensor B is blocked. Replace it as described in

“Replacing a Pressure Sensor for the PLU Pump” on page 90.

6 Troubleshooting
Troubleshooting the Autosampler Aspiration and Calibration

Troubleshooting the autosampler aspiration requires these tools and materials:
• 1/4 in. open-ended wrench
• Powder-free safety gloves
• Sample vial filled with solvent A
• Microtiter plate (if you are using a microtiter plate format)
 To troubleshoot the autosampler aspiration of sample into the needle
1. Make sure that the W3 wash bottle contains sufficient solvent.

2. Use the Flush Air script to remove air from pump S as follows:
c. In the Name list, select Flush Air.
e. Select the Flush Pump S check box.
f. For Flush Threshold [μL], enter 10 for the PLF model pump
or 12 for the PLU model pump (see Figure 231).
Figure 231. Flush Air script

6 Troubleshooting
g. Press Start.
The script runs until the flush threshold reaches the specified value or one of these
error messages appears on the Output page:
• Aborting unable to build pressure
• Aborting check solvent level
3. Depending on whether the Flush Air script passed or failed, do one of the following:
• If the Flush Air script failed, leave the Maintenance > Scripts page open and go to
step 4 to determine if the autosampler needle is blocked.
• If the Flush Air script passed, leave the Maintenance > Scripts page open and go to
step 5 to determine if the autosampler requires calibration.
4. To determine if the autosampler needle is blocked, do the following:
a. Using a 1/4 in. open-ended wrench, disconnect the PEEKsil autosampler needle
from port 1 of valve S.
b. Disconnect the Teflon waste line from port 3 of valve W and connect it to port 1 of
valve S.
c. Place the free end of the Teflon line in an HPLC vial filled with solvent A.
d. To open the Purge script, select Purge in the Name list.
e. Select the Purge Pump S check box.
f. Press Start.
g. Verify that pump S aspirates solvent from the HPLC vial.
h. Do one of the following:
• If pump S can aspirate solvent through the Teflon waste tubing, the needle is
blocked. Reconnect the Teflon waste tubing to port 3 of valve W and replace the
autosampler needle (see “Replacing the Autosampler Needle” on page 84).
• If pump S cannot aspirate solvent through the Teflon waste tubing, go to
“Troubleshooting a Pump that Fails the Flush Air Script” on page 212.
5. To determine if the autosampler needle is going to the correct position and depth, go to
“Checking Sample Pickup” on page 263.

6 Troubleshooting
Checking Sample Pickup
Checking Sample Pickup

When you run the Sample Pickup script, the autosampler withdraws a specified volume from
a specified position. To verify the volume withdrawn by the autosampler, you must place a
known volume into the specified position, and then measure the remaining volume after you
run the script. You can use a pipette or an analytical balance with microgram accuracy to
determine the initial and final volumes.
 To check sample pickup from a microtiter plate or vial
1. Fill the well or vial with a 12 μL of solvent A.

2. Weigh the microwell plate or vial.
3. Insert the tray into the tray compartment.
4. Press Maintenance > Scripts.
5. Run the Sample Pickup script with a pickup volume of 10 μL and your default flow
(see Figure 232).
Figure 232. Sample Pickup script under the Maintenance menu tab
6. After the EASY-nLC application finishes the script, do the following:

a. Eject the tray.
b. Check that 2 μL is left in the well or vial by reweighing the microplate or vial or by
checking the volume with a pipette.
c. If more than 2 μL remains, recalibrate the autosampler, run the Flush Air script, and
then rerun the sample pickup check.
For information about calibrating the autosampler, see Chapter 7. For information
about the Flush Air script, see “Prepare – Flush Air” on page 33.

6 Troubleshooting
Troubleshooting Communication Problems

To troubleshoot communication problems, see these topics:
• “Network Access” on page 264
• “Network Connection Failures” on page 265
• “Testing the Network Connection to the EASY-nLC Computer” on page 266
Network Access
Table 25 contains troubleshooting tips for network access problems.
Table 25. Network access problems
System is not responding after Length of completion time to As indicated, wait while the system changes the
pressing Save Configuration on update the network settings network settings.
the Network page under
Configuration.
Cannot access the EASY-nLC Changed network address Check the network address of the EASY-nLC
system through the network. system on the Configuration > Network page.
The stand-alone EASY-nLC Connect the stand-alone EASY-nLC instrument
instrument is not connected to to a laboratory LAN port with intranet access.
a laboratory LAN port with
intranet access.
The LC/MS system is not Connect the data system computer for the
connected to a laboratory LAN LC/MS system to a laboratory LAN port with
port with intranet access. intranet access.

6 Troubleshooting
Network Connection Failures

Table 26 lists the possible causes of a network connection failure. Figure 233 shows the
Thermo EASY-nLC Configuration dialog box that you access from the Thermo Foundation
Instrument Configuration application. When the EASY-nLC instrument cannot establish
communication with the data system computer, the Connection Failed message appears when
you click Test Connection.
Figure 233. Network connection failure

6 Troubleshooting
Table 26. Possible causes of a network connection failure

The connection between the The network connection has Test the network connection as described in
EASY-nLC instrument and the been unexpectedly disabled. “Testing the Network Connection to the
virtual interface for the Xcalibur EASY-nLC Computer” on page 266.
data system fails.
Close down the EASY-nLC instrument as
described in “Closing Down the EASY-nLC
Instrument” on page 21, and then turn off the
power. Restart the Xcalibur data system
computer. Turn on the EASY-nLC instrument
and log in as an administrator. Retest the
connection.
An antivirus program is Test the connection.
blocking port 6666.
Make sure that the data system computer is not
connected to the Internet, and then uninstall the
antivirus program.
The network firewall is Test the connection.
blocking port 6666.
Remove the firewall.
Connection between the data Test the connection.
system computer and the
EASY-nLC instrument has been
lost.
Testing the Network Connection to the EASY-nLC Computer

If the connection between the EASY-nLC instrument and the data system computer fails
when you click Test Connection in the Thermo EASY-nLC Configuration dialog box of the
Foundation Instrument Configuration window, follow this procedure.
 To test the network connection between the data system computer and the EASY-nLC
instrument
1. From the Windows Start menu, choose Run.
The Run dialog box opens.
2. In the Open box, type cmd.
3. Press OK.
The Command Prompt window opens.
4. Type telnet IP address for the EASY-nLC system 6666 (see Figure 234).

6 Troubleshooting
Figure 234. Command Prompt window with the default IP address for the EASY-nLC instrument
5. Press the ENTER key.

• If the connection is set up correctly, a login prompt appears in the Telnet window
(see Figure 235).
• If the connection is not set up correctly, the following message appears:
Could not open connection to host.
Figure 235. Telnet window with login prompt

6 Troubleshooting
Verifying that the LC/MS System Is Properly Grounded
Verifying that the LC/MS System Is Properly Grounded

When you use the EASY-nLC instrument as an inlet to an MS detector, the LC/MS system
might require two or more fourplex outlets. The interconnected electrical outlets must have a
common point to one ground connector. Connecting the hardware to external grounds at
different potentials can create a ground loop that causes noise and interference and can
damage the contact closure relays on the instrument’s back panel.
IMPORTANT The EASY-nLC instrument, the MS or LC detector, and the (optional)

data system hardware must have a common ground for several reasons:
• Improper grounding or no grounding can result in shock and fire hazards in case of
instrument malfunction.
• Connecting the hardware to external grounds at different potentials can create a
ground loop that causes noise and interference.
• Improper grounding or no grounding can damage the contact closure relays on the
instrument’s back panel. Fixing damaged relays requires the replacement of the
instrument’s built-in computer.
CAUTION Electrical safety regulations require that the EASY-nLC instrument be

grounded to prevent electrical shock and a fire hazard in case of malfunction.
 To verify a common ground between the EASY-nLC instrument and external hardware
1. Connect the EASY-nLC instrument to line power, but do not turn on the instrument.
2. Using a multimeter, measure the resistance between the EASY-nLC chassis and the
external hardware chassis (for example, the mass spectrometer chassis or the data system
computer) as follows:
a. Connect one probe to an unpainted surface on the EASY-nLC chassis and
connect the other probe to an unpainted surface on the external hardware chassis
(see Figure 236).
Figure 236. Resistance measurement
Multimeter set up
to take a resistance
measurement
b. Ensure that the resistance measurement is from 0 to 10 ohms.

7
Calibrating the Autosampler’s XYZ Robot

To calibrate the autosampler’s XYZ robot, follow the instructions in this chapter.
Contents
• Replacing the Autosampler Adapter Plate
• Managing Plate Formats
• Preparing the Autosampler for the Calibration Routines
• Calibrating Plates
• Calibrating the Wash Bottle and Extra Vial Positions
For the ASC autosampler, the calibration covers the following areas of the autosampler.
Microtiter plate or vial plate
Extra vials
Waste bottle
with needle
wash insert
Wash solvent bottles

7 Calibrating the Autosampler’s XYZ Robot
Replacing the Autosampler Adapter Plate
For the legacy ASA autosampler, the calibration covers the following areas of the autosampler.
Microtiter/target Wash/waste
plate bottles
Calibrate the autosampler in the following situations:

• When you want to use a new type of vial or microwell plate.
• When you would like to replace the needle.
• For problems with sample pickup; for example, the needle is not placed in the center of
the well, or not all of the liquid is picked up from one or more of the vials.
• For problems with the wash/waste bottles; for example, the needle is not placed in the
center of the bottle.

The EASY-nLC system ships with the vial adapter plate installed. The microtiter adapter plate
comes in the accessory kit. To load microtiter (microwell) plates into the tray compartment,
you must replace the vial adapter plate with the microtiter adapter plate.
The vial adapter plate holds 48 vials + 6 extra vials. The microtiter adapter plate holds one
96-well plate or one 384-well plate.
Follow the procedure for the autosampler model in your EASY-nLC system to switch between
the two adapter plates as necessary.
• “Replacing the Adapter Plate in the ASC Model Autosampler” on page 271
• “Replacing the Adapter Plate in the ASA Model Autosampler” on page 272

Replacing the Adapter Plate in the ASC Model Autosampler

The ASC model is the current autosampler model for both the EASY-nLC II and the
EASY-nLC 1000 systems.
 To replace the adapter plate in the ASC model autosampler
1. Press Home > Overview.

The Overview page of the Home menu opens.
2. Make sure that the area in front of the tray compartment is clear, and then press
Eject Plate.
The tray compartment opens. Figure 237 shows the vial adapter plate mounted to the
tray holder. The four studs on the bottom side of the plate fit snugly into the mounting
holes on the tray holder.
Figure 237. Open tray compartment
3. Remove the current adapter plate by pulling it up and away from the tray holder
(see Figure 238).
Figure 238. Removing the vial adapter plate before installing the microwell plate adapter plate
Mounting stud
4. Install the other adapter plate in the autosampler.

Replacing the Adapter Plate in the ASA Model Autosampler

The ASA model autosampler is the original autosampler installed in the EASY-nLC II system.
 To replace the adapter plate in the ASA autosampler
1. Eject the tray as follows:

b. Press Eject Plate.
Figure 239 shows an ejected tray.
Figure 239. Tray compartment of the ASA model autosampler
2. Using the 2.5 mm hex wrench provided with your system, remove the screws that secure
the plate to the tray.
The adapter plate is mounted with 4 or 6 hex screws as shown in Figure 240.
Figure 240. Screws that secure the adapter plate to the tray
4 hex screws 6 hex screws

3. Place the new adapter plate on the tray (see Figure 241).
Figure 241. Tray for the ASA model autosampler
4. Fasten the screws in the following balanced order:

a. Screw in the upper right corner.
b. Screw in the lower left corner.
c. Screw in the upper left corner.
d. Screw in the lower right corner.
e. Screws in the middle.
Note Mounting the screws in a balanced order can avoid distortion of the adapter plate.
The autosampler is now ready for new plate formats. For information about selecting a plate
format and creating a new plate format, see “Managing Plate Formats” on page 274. After you
create a new plate format, perform the calibration routines described in this chapter.

Managing Plate Formats

When the EASY-nLC system is initially installed, the application includes plate formats for
vials and microtiter plates
Follow the appropriate procedure to use an existing plate format, create your own plate
format, or delete a plate format that you no longer need.
• “Selecting a Plate Format,” on this page
• “Creating a New Plate Format” on page 275
• “Deleting a Plate Format” on page 277
Selecting a Plate Format

 To select the plate format that you want to use
1. Open the Tools view for the autosampler as follows:

b. In the Devices list, select the autosampler device.
c. Press the Tools tab.
Figure 242 shows the Tools view for the autosampler.

Figure 242. Tools view for the autosampler
Copy To Calibrate Selected plate format

button button
2. Select a plate format from the Plate list.
3. Press Use.
Tip If you are using a Thermo Scientific software application to control your liquid
chromatograph/mass spectrometer (LC/MS) system, the plate selection for the
EASY-nLC system in your Thermo Scientific instrument control software must match
the touch-screen application selection.
Creating a New Plate Format

 To create a new plate format

b. In the Devices list, select the autosampler device.
Figure 242 shows the Tools view for the autosampler.


• To create a new plate format, go to step 3.
• To copy an existing plate format (copies the format selection), go to step 4.
3. Create a new plate format as follows:
a. Press New.
The Create New Plate Format dialog box opens (Figure 243).
Figure 243. Create New Plate Format dialog box
b. In the Format list, select a plate format: 6 × 8 (vials), 8 × 12 (96-well plates), or

16 × 24 (384-well plates).
c. In the Name box, enter a name for the new plate format.
d. Press Accept.
The new plate name appears in the plate list with the text [uncalibrated] appended on
the right.
e. Go to “Calibrating Plates” on page 280 to calibrate the vial or well positions.
4. Copy an existing plate format as follows:
a. Select an existing plate format from the Plate list.
b. Press Copy To.
The Copy Plate Format dialog box opens.
c. In the Name box, type a name for the new plate format.
d. Press Accept.
e. Go to “Calibrating Plates” on page 280 to calibrate the vial or well positions.

Deleting a Plate Format

 To delete a plate format
1. Open the Tools view for the autosampler on the Devices page of the Maintenance menu
(see step 1 on page 275).
2. Select a plate format from the Plate list.
Note You cannot delete the plate in use. When you select the plate in use (highlighted
in bold text), the Delete button becomes unavailable.
3. Press Delete.
The Delete Plate Data dialog box opens.
4. Press Accept.

Preparing the Autosampler for the Calibration Routines

To prepare the autosampler for the calibration routines, you must remove the left side panel
from the instrument and load the appropriate adapter plate, vials or microtiter plate, wash
bottle (W4) with insert, and (optional) extra vial into the tray compartment.
CAUTION Calibrating the autosampler requires removal of the side plate and visual
inspection of the autosampler needle holder. Because the autosampler compartment
contains moving parts and sharp needles, make sure to keep hands clear when operating
the autosampler during calibration.
 To prepare the autosampler for the plate calibration routine
1. Install the appropriate adapter plate.

2. To calibrate the vial or well positions on a plate, do one of the following:
• To calibrate the 6 × 8 vial positions, remove the vial caps from two vials and load
them into the adapter plate in positions A1 and F8.
• To calibrate a microwell plate, remove the mat or cover from the microwell plate and
load the microwell plate onto the adapter plate.
b. In the Devices list, select the autosampler.
4. In the Plate area, do the following:
a. Select the appropriate plate format from the list, or create a new plate format
(To create and select plate formats, see “Managing Plate Formats” on page 274).
b. Press Use.
5. Remove the left side panel so that you can watch the movement of the needle.
To calibrate the plate, go to the next topic “Calibrating Plates.”
 To prepare the autosampler for the V1 and W4 calibration routine
1. Place an empty vial in position V1.

The V1 position is not available for the microtiter plate formates.
2. Prepare the bottle for position W4 (used for ejecting waste and cleaning the outside of the
injection needle).
3. For information about preparing the W4 wash bottle, refer to the EASY-nLC Series
Getting Started Guide.

4. Install the wash bottle in position W4.
IMPORTANT For the autosampler to determine the appropriate depth for the
needle, the wash bottle in position W4 must contain the needle wash insert.
5. Remove the left side panel so that you can watch the movement of the needle.
To calibrate the wash bottle and extra vial positions, go to “Calibrating the Wash Bottle and
Extra Vial Positions” on page 285.

Calibrating Plates
Calibrating Plates
For information about selecting or creating a plate format, see “Managing Plate Formats” on
page 274.
IMPORTANT When calibrating the XYZ robot for vial or microwell plates, make sure to
remove the vial caps or plate covers. Keeping the caps or covers on makes the needle
susceptible to bending.
During a sample run, the z-axis needle holder moves to the specified sample position along
the xy-plane. When the z-axis needle holder reaches the specified location, the needle descends
along the z-axis into the sample vial or well.
Calibrating plates requires determining the xyz positions for the top left and bottom right vial
or well. Table 27 lists the top left and bottom right positions for the three plate formats.
Table 27. Top left and bottom right positions on the plate formats
Plate format Top left position Bottom right position
6×8 A1 F8
8 × 12 A1 H12
16 × 24 A1 P24
 To calibrate plates
1. If you have not already done so, prepare the autosampler for the plate calibration routine
(see “To prepare the autosampler for the plate calibration routine” on page 278).
2. Open the Autosampler Plate Calibration dialog box as follows:
The Tools view opens (see Figure 244).
Figure 244. Tools view for the autosampler

Calibrating Plates
d. In the Plate area of the Tools view for the autosampler, press Calibrate
The Autosampler Plate Calibration dialog box opens.
Figure 245 shows the dialog box at the beginning of the plate calibration routine.
The top left and bottom right positions are highlighted in green. The position
readbacks for the xyz axes are unpopulated, .
Figure 245. Plate view in the Autosampler Plate Calibration dialog box
(3) (1) (5)
(2)
(4)
3. Press the green vial or well in the upper left corner of the plate view (1).
The needle moves to the current saved coordinate. The saved coordinates for the x and
y axis appear on the left side of the slash, the needle does not descend into the vial or well,
and the z-axis value on the left side of the slash remains at 0.
The values on the left side of the slash change as you adjust the needle position.

Calibrating Plates
4. Center the needle above the vial or well as follows:

• Press the Needle In/Out (3) buttons to adjust the x-axis position.
• Press the Needle Left/Right (4) buttons to adjust the y-axis position.
y axis 1
In
A
x axis
Out
Right
Left
5. Using the step buttons in the Needle Up/Down area (5), adjust the needle height as
follows:
a. Using the big step button (), lower the needle until it reaches a level of 2–3 mm
(0.08–0.12 in.) above the vial or well.
b. Using the small step button (), slowly lower the needle until it reaches the bottom of
the vial or well.
Tip For the ASC autosampler, the O-ring at the top of the needle holder rises a
little when the needle reaches the bottom of the vial or well (see Figure 246).
Figure 246. O-ring pushed slightly above the ASC needle holder
Observe when the O-ring moves up a

bit, or gently hold needle tubing as you
press the step button.

Calibrating Plates
Tip For the ASA autosampler, do one of the following to determine the bottom
position of the vial or well:
• To feel when the needle reaches the bottom of the vial or well, hold the
needle gently as you press the down arrow on the touch-screen interface.
• To see when the needle reaches the bottom of the vial or well, draw a mark on
the needle and observe the needle mark as you press the down arrow on the
touch-screen interface. When the needle mark moves up a bit, the needle has
reached the bottom of the vial. Figure 247 shows the ASA needle holder and
needle.
Figure 247. ASA autosampler needle holder
Use a black marker pen to

make a line on top of the
PEEKsil tubing.
c. Press the small step button () once to raise the needle slightly off the bottom of the
vial or well.
The appropriate needle height is one small step higher than the bottom of the vial
or well.
6. When you are satisfied with the current xyz-coordinate for the vial or well, press Capture.
The color of the vial or well on the plate graphic changes from green to red and the
position readbacks for the xyz axes are unpopulated, (see Figure 248).

Calibrating Plates
Figure 248. Plate calibration captured for the A1 position
7. Press the green vial or well in the lower right corner of the plate view.
y axis appear on the left side of the slash, the needle does not descend into the vial or well,
and the z-axis value on the left side of the slash remains at 0.
8. Repeat step 4 through step 6 on that vial or well.
9. Press Save and then press Close to close the calibration dialog box.
10. Replace vial caps and plate covers as necessary.
11. Go to the next procedure to calibrate the W4 bottle position or reinstall the EASY-nLC
instrument’s left side panel.
IMPORTANT To maintain a stable temperature inside the tray compartment, the

left side panel must be installed.

Calibrating the Wash Bottle and Extra Vial Positions

In addition to holding the sample trays, the EASY-nLC tray compartment holds four wash
bottles (W1–W4) and six extra vials (V1–V6).
 To calibrate the W4 wash bottle position, the extra vial positions, or both
1. If you have not already done so, prepare the autosampler for the extra vial and wash bottle
calibration as described in “To prepare the autosampler for the V1 and W4 calibration
routine” on page 278.
2. Open the Autosampler Vials/Wash Calibration dialog box as follows:
c. Press the Tools tab below the Devices list.
d. In the Vials/Wash area, press Calibrate.

The Autosampler Vials/Wash Calibration dialog box opens (see Figure 249).
3. Press the bottle container in W4 (1) (see Figure 249).
y axis appear on the left side of the slash, the needle does not descend into the bottle, and
the z-axis value on the left side of the slash remains at 0.
Figure 249. Vials/Wash view in the Autosampler Vials/Wash Calibration dialog box
(2)
(5)
(4)
(1)
(3)

4. Center the needle above the bottle as follows:

• Press the Needle In/Out (2) buttons to adjust the x-axis position.
• Press the Needle Left/Right (3) buttons to adjust the y-axis position.
y axis
In
x axis
Out
Right
Left
5. Using the step buttons in the Needle Up/Down area (5), adjust the needle height as
follows:
a. Using the big step button (), lower the needle until it reaches a level of 2–3 mm
(0.08–0.12 in.) above the bottle.
b. Using the small step button (), slowly let the needle enter the hole and lower the
needle until it reaches the bottom of the wash insert in the bottle.
Note The O-ring at the top of the needle holder rises a little when the needle
reaches the bottom of the well.
c. Press the large step button () twice to raise the needle off the bottom of the wash
bottle insert.
Two large steps higher than the bottom of the wash bottle insert is the appropriate needle
height.
Note The ASA autosampler has a limit of 850 steps on the z axis (vertical). This limit
is set to avoid bent needles. You might be able to go for more than 850 steps during
calibration, but the needle does not go more than 850 steps during normal work.
6. Press Capture when you are satisfied with the current xyz-coordinate for position W4.
The color of the bottle container number changes from green to red.
7. (Optional) To calibrate the extra vial positions for the 6 × 8 plate format, do the
following:
a. Press V1 vial (5) to select it.
b. Repeat step 4 through step 6 for vial V1.
8. Press Save and then press Close to close the calibration dialog box.

8
Remote Support
The EASY-nLC instrument includes a remote support feature that enables Thermo Fisher
Scientific Technical Support to diagnose and troubleshoot your EASY-nLC system remotely
while the instrument is connected to the support server. When you connect the instrument to
the remote server, you can also install the latest firmware file for the touch-screen application.
Technical Support cannot initiate the communication link between your

EASY-nLC instrument and the support server. You must initiate this communication link
from your EASY-nLC instrument.
To connect the EASY-nLC instrument to the support server or download system files to a
removable storage device, follow these procedures.
Contents
• Connecting the EASY-nLC Instrument to the Support Server
• Saving System Files on a USB Removable Storage Device
• Downloading the Latest Firmware File
IMPORTANT To establish communication with the support server, you must first
connect the EASY-nLC instrument directly to your local network, and then open the
communication link for remote support through the touch-screen software. Thermo
Fisher Scientific Technical Support cannot initiate this communication link.
The EASY-nLC instrument uses Secure Shell (SSH™), a network protocol for
secure data communication, to connect to the support server, which uses the Linux™
operating system.
To use the remote support feature, the firewalls for your local network must allow
outgoing TCP/IP traffic from the EASY-nLC system to the support server at
IP address 195.41.108.93 port 22.
When you establish the communication link with the support server, the support server
triggers the file compression utility on the EASY-nLC instrument to build a zip file with
the appropriate log files, and then retrieves the zip file from the EASY-nLC instrument.
Meanwhile, the EASY-nLC instrument sends an e-mail with your supplied message and
contact information to Thermo Fisher Scientific Technical Support.
After you send a message through the remote support feature, a member of the Thermo
Fisher Scientific Technical Support team will contact you.

8 Remote Support
Connecting the EASY-nLC Instrument to the Support Server

Use this procedure to establish a communication link between the EASY-nLC instrument’s
computer and the support server.
 To open a communication link between the EASY-nLC system and the support server
1. Using a shielded Ethernet cable, connect the LAN port on the back panel of the
EASY-nLC system (see Figure 250) directly to a laboratory LAN port that provides access
to the Internet.
To use the remote support feature, the firewalls for your local network must allow
outgoing TCP/IP traffic from the EASY-nLC system to the support server at
IP address 195.41.108.93 port 22.
Figure 250. Ethernet connection between the EASY-nLC system and the laboratory LAN port
P-BUS
HARD
DRIVE
I
O
110-120V▼
LAN port with
120/230 V : 50/60 Hz: 250 W

Fuse at 120 V– : T5 AL 250 V
Internet capability
Fuse at 230 V– : T2.5 AL 250 V
2012

8 Remote Support
2. If you have not already set up the support server configuration, set it up as follows:
a. Press Configuration > Network.
The Network page of the Configuration menu opens (Figure 251).
Figure 251. Network page of the Configuration menu
b. In the LAN area, do the following:

i. Select Internet in the Profile list.
ii. Press Apply.
c. In the Support Server area, do the following:
i. Enter the following IP address: 195.41.108.93.
ii. Press Apply.

8 Remote Support
3. Send a support request message and a zip file containing the appropriate log files to
Technical Support as follows:
a. Press Maintenance > Support.
The Support page of the Maintenance menu appears (see Figure 252).
Figure 252. Support page of the Maintenance menu
b. In the Connect to EASY-nLC Support area, press Connect.

Depending on whether the instrument has the latest firmware file installed, one of
these dialog boxes appears:
• If the instrument has the latest firmware file installed, the Message to Support
Team dialog box appears (see Figure 253).
• If the instrument does not have the latest firmware file installed, the Upgrade is
Available dialog box appears (see Figure 256 on page 296).
c. If the Upgrade is Available dialog box appears, do one of the following:
• Upgrade the software as described in “Downloading the Latest Firmware File” on
page 296.
–or–
• Click Skip.
The Message to Support Team dialog box appears.

8 Remote Support
d. Select a support region, provide valid contact information, and describe the problem
that you are experiencing.
Figure 253. Message to Support Team dialog box
Note When you place the cursor in the Phone Number box, the program
prompts you for a country code and phone number.
Tip When you place the cursor in the Email Address box, the program prompts
you to enter an address in this format: name@company.com.
To enter the @ symbol, press Shift. The numbers row changes to the symbols
row. Then press @.
e. Press Accept.
After you enter the requested information, the Status box on the right side of the
Support page should change from Not Connected to Connected.

8 Remote Support
f. Depending on the connection status, do one of the following:

• If the status changes from Not Connected to Connected, go to step 3g.
• If the connection fails, see “To troubleshoot a failed connection to the support
server” on page 292.
When the connection fails, the SSH Connection Error dialog box might
appear with this message, “Not able to determine connection status. See
message.log for details.”
The message.log file is in the admin\systemLog folder on the EASY-nLC
system. For information about accessing the admin folder from another
computer on your local network, refer to the EASY-nLC Series Getting Started
Guide.
While the message.log file might provide useful information to a member of
Thermo Scientific Technical Support, users should follow the suggested
troubleshooting procedure, “To troubleshoot a failed connection to the support
server” on page 292.
g. After the status changes to Connected, allow enough time for the EASY-nLC system
to create the zip file in the admin folder and for the support server to retrieve the zip
file. Then go to step 4.
After you send a message with the appropriate contact information through the
remote support feature, a member of the Thermo Fisher Scientific Technical Support
team will contact you.
4. To close the communication link, press Disconnect.
5. To return the system to normal operation, do the following:
a. Reconnect the Ethernet cables as appropriate.
For information about connecting the EASY-nLC system to a data system computer,
refer to the EASY-nLC Series Getting Started Guide.
b. In the LAN area of the Configuration > Network page, do the following:
i. Select LAN in the Profile list.
ii. Press Apply.
 To troubleshoot a failed connection to the support server
1. Check the support server configuration (see step 2 on page 289).

2. Verify that the Ethernet cable is securely connected to both the LAN port on the back
panel of the EASY-nLC system and the laboratory LAN port.
3. Verify that the Ethernet cable is working.
4. Ask your IT administrator if the network firewalls allow outgoing traffic to port 22
through an SSH connection.

8 Remote Support
Saving System Files on a USB Removable Storage Device

The EASY-nLC system includes network capability. Through the network you can back up
your system, export and import batches and methods, analyze your system by examining the
log files, and perform many other tasks. However, when you are not connected to the network
or the network is broken, or you do not have a computer with network access that is near the
EASY-nLC system, you can use the copy function to copy all the system files on the system to
a USB removable storage device, such as a USB flash drive or memory stick.
The EASY-nLC system ships with a USB flash drive for your convenience. But you can use
any USB storage device formatted with the file system FAT/FAT16 and at least 128 MB of
free space.
 To copy system files to a USB storage device
1. Press Maintenance > Support.

The Support page of the Maintenance menu opens (see Figure 252 on page 290).
2. Insert the USB storage device into the connector panel on the back of the EASY-nLC
instrument. Choose between one of two USB ports on the upper left side of the panel
(see Figure 254).
Figure 254. USB port location on the back panel of the EASY-nLC instrument
3. In the Log File Copy area, select the To USB Removable Storage option.
Note When you select the To Home Directory option, the EASY-nLC system creates
zip files in the admin folder.
For information about accessing the admin folder from another computer on your
local network, refer to the EASY-nLC Series Getting Started Guide.

8 Remote Support
4. Press Copy Log Files.

When the copying is finished, the following confirmation appears.
5. Press Close and remove the USB storage device from the connector panel.
6. Insert the USB storage device into your computer.
Five zipped files appear on the USB storage device (see Figure 255 and Table 28 on
page 295).
Figure 255. Windows XP view of the files on the USB memory stick

8 Remote Support
Table 28. Zipped files created by pressing Copy Log Files

File name Description
batchlog.zip Contains one folder for each batch you have run with
information on samples, methods, and EASY-nLC device
performance.
etc.zip Contains system configuration files.
export.zip Contains exported batches and methods per user and system
backup.
logfiles.zip Contains system log files with information on overall system
performance.
maintlog.zip Contains one folder for each maintenance script you have run
with information on EASY-nLC device performance.
If you have problems with your system, forward the files to Thermo Fisher Scientific
Technical Support for assistance.

8 Remote Support
Downloading the Latest Firmware File

If the EASY-nLC instrument does not have the latest version of the touch-screen application,
connect the instrument to the remote server and install the appropriate firmware files as
described in the following procedure.
 To install the latest firmware file
1. If the instrument is not already connected to the remote server, connect the instrument as
follows:
a. From the touch screen, press Maintenance > Support.
The Support page of the Maintenance menu appears.
b. In the Connect to EASY-nLC Support area, press Connect.
If the EASY-nLC instrument does not have the latest version of the touch-screen
application, the Upgrade is Available dialog box appears.
Figure 256 shows the message for an instrument with firmware version 2.4.
Figure 256. Firmware upgrade message
2. Click Download.
When the file transfer is complete, the Transfer of Log and Firmware Files Completed
dialog box appears.

8 Remote Support
Figure 257 shows the transfer information for an instrument with firmware version 2.4.
Figure 257. Information for upgrading from a previous version
3. Click OK.
4. To begin the firmware upgrade, do the following:
a. Press Exit in the lower-left corner of the touch screen.
A confirmation dialog box opens (see Figure 22 on page 21).
b. Press Power Down.
The EASY-nLC application displays a white screen with a small progress bar. When
the progress bar is completely filled, a message appears indicating you can safely turn
off the instrument.
c. Turn off the instrument, and then turn it back on.
d. When the Upgrade button appears, double-tap it.
5. If the complete upgrade requires more firmware files, reconnect to the server and install
the upgrade files as described in step 1 through step 4 of this procedure.
Table 29 lists the software versions that you must install to upgrade the software to the
current version.
Table 29. Software installation matrix
Current version Install versions
2.4 #2923 2.5 #3032, 2.7.8.1, 2.8.11.1, and 3.1.4.1
2.5 #3032 2.7.8.1, 2.8.11.1, and 3.1.4.1
2.7.8.1 2.8.11.1 and 3.1.4.1
2.8.11.1 3.1.4.1
3.1.4.1 current as of January 2013

9
Returning the EASY-nLC Instrument

If it is necessary to return the EASY-nLC system to the factory, follow the instructions in this
chapter.
Contents
• Transport Instructions
• Declaration of Contamination
Transport Instructions
 To prepare the instrument for transport
1. Press Home > Overview.

2. Press Eject Plate.
3. Remove the plates/tubes.
4. Remove the waste beaker and the wash/waste bottles.
5. Press Insert Plate.
6. Close down the system (see “Closing Down the EASY-nLC Instrument” on page 21).
7. Remove the cables on the back side.
Tip For the original ASA autosampler only: Secure the autosampler by using the
transport collars (see Figure 258) before shipping the instrument. (This is not
necessary on the latest ASC model.)

9 Returning the EASY-nLC Instrument
Transport Instructions
Figure 258. (ASA autosampler only) Transport collar location
Insert two
transport collars
after closing
down the
instrument.
8. Fill out the Declaration of Contamination of Equipment in “Declaration of

Contamination” on page 301.
9. Place the EASY-nLC instrument in the original shipping container.

9 Returning the EASY-nLC Instrument
Declaration of Contamination
Declaration of Contamination
To return, service, or repair the EASY-nLC instrument, you must complete and submit a
“Declaration of Contamination of Equipment” to Thermo Fisher Scientific with the returned
equipment. Qualified personnel must review the declaration. Contact Thermo Fisher
Scientific for additional copies of this form or if you have any questions regarding the
contents of this declaration.
Description of equipment
Equipment type/model: ______________________ Serial No.: __________________
Date of receiving/purchasing equipment: _________________________
Reason for return: [ ] Maintenance [ ] Repair [ ] End of test
[ ] ______________________________________
Describe symptoms and problems: ___________________________________________
______________________________________________________________________
Equipment condition
Has the equipment been used? [ ] Yes [ ] No
Has the equipment been exposed to potentially harmful substances?
[ ] Yes [ ] No
If yes, attach list of all known harmful substances including chemical name and symbol, and
precautions associated with the substances.
Were any of the harmful substances
• Radioactive? [ ] Yes [ ] No
• Toxic? [ ] Yes [ ] No
• Corrosive? [ ] Yes [ ] No
• Explosive? [ ] Yes [ ] No
Has the equipment been properly decontaminated and/or cleaned before being returned?
[ ] Yes [ ] No
Legally binding declaration
I hereby declare that the information supplied on this form is accurate and sufficient to
judge any contamination level.
Name: ________________________________________________________________
Job title: ____________________ Organization: _____________________________
Address: _______________________________________________________________
Telephone: ________________ Fax: ________________ E-mail: __________________
Signature: ______________________________________________________________

A
Error Codes
Table 30 lists the possible error codes.
Table 30. Error codes (Sheet 1 of 8)

No. Issue code name Description Cause Solution
1 ERROR_IO_CLOSING_ Failed closing log file File system error Internal filesystem error -
FILE Replace the hard drive.
2 ERROR_IO_WRITING_ IOException I/O error occurred Internal filesystem error -
TO_FILE Replace the hard drive.
3 ERROR_IO_NO_FILE_ Log was closed trying to Filesystem error Internal filesystem error -
OPEN log the following message: Replace hard drive
4 ERROR_IO_CREATE_ Failed creating log file I/O error occurred Internal filesystem error -
FILE 'LOG_FILE_NAME' Replace the hard drive.
5 ERROR_IO_CREATE_ Failed creating log folder I/O error occurred Internal filesystem error -
FOLDER 'LOG_FOLDER_NAM Replace the hard drive.
E'
6 ERROR_IO_FILE_ Failed creating log Filesystem error Internal filesystem error -
EXISTS 'LOG_FILE_NAME Replace the hard drive.
AND_PATH' (file
already exists)
7 ERROR_IO_FILE_CAN Failed creating log Filesystem error Internal filesystem error -
NOT_WRITE ''LOG_FILE_NAME_ Replace the hard drive.
AND_PATH' (file not
writable)
8 ERROR_BATCH_BEIN It appears the current [see issue description] Close or reschedule the
G_EDITED batch is being edited, batch.
please close or reschedule
it.
9 ERROR_DEVICE_ Failed accessing device Missing the hardware Add the device to
ACCESS_FAILED DEVICE_ID component driver the list on the Maintenance
> Devices page.

A Error Codes

10 ERROR_PREP_ Pump B unable to Pump unable to reach Check that solvent bottle is
GRADIENT_ reach 90% A pressure set pressure during not empty and check for air
PRESSURE_BUILD_ within 30 μL. prep gradient and leaks in the system.
FAILED Please check for air/leaks!
11 ERROR_PUMP_ stopped (out of solvent). Out of solvent Refill the solvent reservoir
STOPPED_EMPTY bottle. Check for air and
leaks in the system.
12 ERROR_PUMP_ stopped unexpectedly Pump hardware issue Check the pump
STOPPED_ (unknown cause). functionality.
UNEXPECTEDLY
26 ERROR_QUEUE_ Current queue element is Trying to execute a job Close or reschedule the
ELEMENT_BEING_ being edited; stopping. currently being edited batch.
EDITED
27 ERROR_PBUS_IN_ P-BUS interface in service Trying to initialize the Check that the RS485
SERVICE_MODE mode. RS485 interface while switch on PC is in the
serial port is in the ON position.
service mode
28 ERROR_PBUS_ Initialization of P-BUS [see issue description] Troubleshoot P-BUS
INTERFACE_INIT interface failed communication -
Check that the cables are
properly connected.
29 ERROR_PBUS_ Error writing to interface [see issue description] Troubleshoot P-BUS
SEND_BYTES COMM_PORT communication -
properly connected.
30 ERROR_PBUS_ Error reading from [see issue description] Troubleshoot P-BUS
READ_BYTES interface COMM_PORT communication -
properly connected.
31 ERROR_SENSIRION_ Failed parsing flow sensor Could not parse some Cycle EASY nLC power.
FACTOR_PARSING factor from string to a double
INFO_COMMAND
32 ERROR_SENSIRION_ Flow sensor factor not Error getting flow Cycle EASY nLC power.
FACTOR_NOT_ found in info output. sensor scaling factor
FOUND Factor unknown.

A Error Codes

33 ERROR_ Port COM_PORT does Error getting input Cycle EASY nLC power.
SENSIRION_ not support reading/Error from flow sensor
INIT getting input stream from
flow sensor port
COM_PORT
34 ERROR_SENSIRION_ No data received from [see issue description] Cycle EASY nLC power /
NO_DATA flow sensor for X seconds Check the flow sensor
functionality.
35 ERROR_SENSIRION_ Flow sensor in Trying to start a flow Cycle EASY nLC power.
IN_MEASURE_MODE measurement mode. Stop sensor that is already
measurements before started
sending further
commands
36 ERROR_SENSIRION_ IO Error while [see issue description] Check the flow sensor
IO communicating with flow communication/cable.
sensor
37 ERROR_SENSIRION_ No response from flow [see issue description] Cycle EASY nLC power -
TIMEOUT sensor (timeout) If the problem persists,
replace the flow sensor.
See “Replacing a Flow

Sensor” on page 92.
38 ERROR_SENSIRION_ Flow sensor echo Flow sensor fails Rare error - Connect the
ECHO_MISMATCH "ECHO" does not match to "talk back" EASY-nLC system to
command remote support.
"COMMAND"
See “Connecting the
EASY-nLC Instrument to
the Support Server” on
page 288.
39 ERROR_SENSIRION_ Flow sensor error: Flow sensor failing, but Rare error - Connect the
BAD_RESPONSE ERROR_MESSAGE/Flo does not report it EASY-nLC system to
w sensor did not respond remote support.
with OK, but did not
report an error either
40 ERROR_SENSIRION_ Cannot calibrate sensor in Flow sensor in idle Cycle EASY nLC power.
IN_IDLE_MODE idle mode mode during Check the flow sensor
calibration functionality.

A Error Codes

41 ERROR_SENSIRION_ Cannot store flows larger Abnormal value trying Cycle EASY nLC power.
CALIBRATION than 9999 nL/min to be written to the Check flow sensor
flow sensor functionality
42 ERROR_RS232_INIT Initialization of interface Access to interface Cycle EASY nLC power.
"PORT_NAME" failed failed
54 ERROR_RS485_ COMPONENT_ID Error occurred when Troubleshoot P-BUS
COMMAND_VERIFY COMMAND failed: sending COMMAND communication/hardware.
ERROR_MESSAGE
55 ERROR_ Unknown rack shelf Unknown rack shelf Verify that the sample
MANIPULATOR_ RACK_SHELF_VALUE position supplied to position is correct.
UNKNOWN_RACK_ driver
SHELF
56 ERROR_ Unknown rack position Could not move to bad Verify that the sample
MANIPULATOR_ id rack position position is correct.
UNKNOWN_RACK_ RACK_POSITION_ID_
POS_ID VALUE
57 ERROR_ Grid configuration Error uploading Calibrated position not
MANIPULATOR_SET_ change failed autosampler plate recognized by software. See
GRID_CONFIG L (AUTOSAMPLER_ calibration Chapter 7, “Calibrating the
RETURN_CODE) (0 = asrOK, Autosampler’s XYZ Robot.”
1 = asrBusy,
2 = asrBadLocation,
3 = asrBadCoordinate,
4 = asrEjected,
5 = asrAxisError,
6 = asrChecksumError)
58 ERROR_ Wash configuration Error while saving Calibrated position not
MANIPULATOR_SET_ change failed autosampler wash recognized by software. See
WASH_CONFIG (AUTOSAMPLER_ calibration (see code 57 Chapter 7, “Calibrating the
RETURN_CODE) for asr codes) Autosampler’s XYZ Robot.”
59 ERROR_ Vial configuration change Error while saving Calibrated position not
MANIPULATOR_SET_ failed autosampler vial recognized by software. See
VIAL_CONFIG (AUTOSAMPLER_RET calibration (see code 57 Chapter 7, “Calibrating the
URN_CODE) for asr codes) Autosampler’s XYZ Robot.”

A Error Codes

60 ERROR_ tray eject failed see code 57 for asr Verify that the correct plate
MANIPULATOR_TRAY (AUTOSAMPLER_RET codes is configured in the
_EJECT URN_CODE) EASY-nLC software and
the Xcalibur VI. Check that
no objects in the tray
compartment are
obstructing the XYZ robot
movement. Reset
manipulator and run the
Torque script for the ASC
model autosampler.
61 ERROR_ tray load failed see code 57 for asr (see above)
MANIPULATOR_TRAY (AUTOSAMPLER_RET codes
_LOAD URN_CODE)
62 ERROR_ grid address failed Could not move to (see above)
MANIPULATOR_GRID (AUTOSAMPLER_RET sample position (see
_ADDRESS URN_CODE) code 57 for asr codes)
63 ERROR_ wash address failed Could not move to (see above)
MANIPULATOR_ (AUTOSAMPLER_RET wash position (see code
WASH_ADDRESS URN_CODE) 57 for asr codes)
64 ERROR_ vial address failed Could not move to vial (see above)
MANIPULATOR_VIAL_ (AUTOSAMPLER_RET position (see code 57
ADDRESS URN_CODE) for asr codes)
65 ERROR_ needle down failed Could not move needle (see above)
MANIPULATOR_ (AUTOSAMPLER_RET down (see code 57 for
NEEDLE_DOWN URN_CODE) asr codes)
66 ERROR_ needle up failed Could not move needle (see above)
MANIPULATOR_ (AUTOSAMPLER_ up (see code 57 for asr
NEEDLE_UP RETURN_CODE) codes)

A Error Codes

69 ERROR_VALVE_SET_ COMPONENT_ID Valve unable to switch Clean the rotor seal and the
POSITION setPosition failed: position stator. Replace the rotor
Unrecognized position seal if necessary.
POSITION/
COMPONENT_ID If the problem persists, do
setPosition failed: the following:
Problems switching to • For valve serial number
position POSITION/ < V-009800, run the
COMPONENT_ID Valve Tune script.
needed ATTEMPTS • For valve serial number
attempts switching to > V-009800, replace
position POSITION the valve.
70 ERROR_PARALLEL_ Contact closure port Contact Thermo Fisher

PORT_WRITE IO error Scientific.
PORT_NOT_ IO error Scientific.
INITIALIZED
PORT_MASS_SPEC_ IO error Scientific.
BUSY
PORT_MASS_SPEC_ IO error Scientific.
TIMEOUT
PORT_INIT IO error Scientific.
PORT_WRONG_PORT IO error Scientific.
77 ERROR_DEVICE_LOW DEVICE: Low voltage [see issue description] Faulty 24V supply -
_24_VOLT_SUPPLY (VALUE V) Connect to remote support
78 ERROR_ DEVICE: Init failed (not [see issue description] Autosampler hardware
MANIPULATOR_INIT ready within 1 minute) issue. Cycle EASY-nLC
power. If the problem
persists, check the P-bus
cables to the autosampler.
79 ERROR_DEVICE_SELF DEVICE: Status bit(s) set Error returned from Connect the system to the
_TEST after self test: hardware component remote support server (see
0xBITS_IN_HEX firmware Chapter 8).

A Error Codes

80 ERROR_DEVICE_IN_ DEVICE: Device in boot Error returned from Contact Thermo Fisher
BOOT_MODE mode after device reset hardware component Scientific.
firmware because a
PCB is damaged.
81 ERROR_PELTIER_ DEVICE: Spurious Cooler sensor defective Replace the cooler.
SPURIOUS_ temperature
TEMPERATURE (TEMPERATURE_IN_ See “Replacing the
DEGREES_CELSIUS) Autosampler Cooler” on
page 137.
82 ERROR_DEVICE_LOW DEVICE: Low current Peltier element Replace the cooler.
_CURRENT consumption defective
(CURRENT_VALUE A)
83 ERROR_VALVE_ DEVICE: Spurious angle [see issue description] For valve serial number
SPURIOUS_ANGLE in position POSITION < V-009800, run the Valve
(ANGLE) Tune script.
84 ERROR_APPLICATION HISTORY_TRACE Application state Cycle EASY nLC power.
_STATE empty or illegal
85 IC_STATUS_FLAG_ Monitor reported Act according to the error
WARNING flag(s) raised (log file message.
only).
86 IC_STATUS_FLAG Monitor reported Act according to the error
_SEVERE flag(s) raised (in user message.
interface, current run
stopped).
87 IC_LC_CONDITION_ Waiting for some Failed reaching a Troubleshoot the LC
UNSATISFIED condition during run specific flow, pressure, system for leaks and air.
unsuccessful. etc. within a specified
volume/period of time. See “Troubleshooting the
Results of the System Leak
Test” on page 221.
88 IC_STATUS_FLAG_ Monitor reported Act according to the error
ERROR flag(s) raised (in user message.
interface).

A Error Codes

89 IC_VALVE_MULTIPLE_ Needed 2 attempts to A switching valve Clean the rotor seal and the
ATTEMPTS switch to position 1-6 needed multiple stator. Replace the rotor
attempts to reach the seal if necessary.
target position.
If the problem persists, do
the following:
• For valve serial number
< V-009800, run the
Valve Tune script.
• For valve serial number
> V-009800, replace
the valve.
90 IC_DEVICE_ A device type operation Contact Thermo Fisher
UNSUPPORTED_ was attempted on a Scientific.
OPERATION device instance that
doesn't support it.
92 IC_BUSINESSLOGIC_ Gradient interrupted by Pump solvent volume No action is necessary.
REFILL_DURING_ pump refill warning too small for next This is just a warning that
GRADIENT gradient step. the pumps were refilled
during gradient processing.
93 IC_SCRIPT_AUTO_ Maintenance script Probably because a Check for air and leaks in
ABORT self-abort pump ran out of the subsystem.
solvent while See “Troubleshooting the
building/maintaining Results of the System Leak
pressure Test” on page 221.

B
Mobile Phase Viscosity

Table 31 lists the viscosities for two-solvent mobile phases consisting of a water/methanol
mixture or a water/acetonitrile mixture.
Table 31. Mobile-phase viscosity at 25 C for reversed-phase gradients
25 (cP)
Mobile phase (%v organic/water) Methanol Acetonitrile
0 0.89 0.89
10 1.18 1.01
20 1.40 0.98
30 1.56 0.98
40 1.62 0.89
50 1.62 0.82
60 1.54 0.72
70 1.36 0.59
80 1.12 0.52
90 0.84 0.46
100 0.56 0.35
Reference: D.P. Herman, A.H. Billiet, and L. de Galan, Journal of Chromatography,
463 (1989) 1

C
Consumables and Replacement Parts

To order consumables and replacement parts for the EASY-nLC system, see the ordering
information and solvent system schematics in this chapter.
Contents
• Ordering Information
• Solvent System Schematic for the EASY-nLC II Instrument
• Solvent System Schematic for the EASY-nLC 1000 Instrument
• Common Replacement Parts
Ordering Information
To obtain ordering information for the EASY-nLC instrument’s spare parts and accessories, go
to the following Web sites:
• For the EASY-nLC 1000 instrument, go to:
http://www.proxeon.com/productrange/nano_lC_easy-nlc_1000/accessories_spares
• For the EASY-nLC II instrument, go to:
http://www.proxeon.com/productrange/nano_lC/accessories_spares
These EASY-nLC parts are consumable parts and not covered by the normal first year Limited
Warranty offered by Thermo Fisher Scientific, or any other service contract agreement
containing extended warranty coverage.
• All flow lines including Tee-pieces and fittings (nuts, ferrules, sleeves, and valve stops)
• Check valves
• Solvent filters, inline filters, and all associated filter holders
• Pump piston seals
• Valve rotors and stators
• All bottles and lids
• All sample vials, microtiter plates, and associated lids and mats
• Columns
• Fuses
• Autosampler needle

C Consumables and Replacement Parts
Solvent System Schematic for the EASY-nLC II Instrument

Table 32 lists the tubing requirements for the EASY-nLC II instrument. The numbers in the
ID column correspond to the numbers in the solvent system schematic shown in Figure 259.
Kit LC230 includes the Teflon tubing and the check valve assembly required to replace the
low-pressure solvent system for one pump. Kit LC243 includes a complete set of flow lines to
the mixing Tee, but does not include the mixing Tee itself.
Table 32. Tubing requirements for the EASY-nLC II system
No. Connections Tubing Part number
1 Pump A outlet to pressure sensor A inlet PEEK, 300 μm ID, 15 cm length LC212
Pump S outlet to pressure sensor S inlet
Pressure sensor A outlet to port 1 of valve A
Pressure sensor S outlet or port 2 of valve S
2 Pump B outlet to pressure sensor B inlet stainless steel, prebent LC215
3 Pressure sensor B outlet to port 1 of Valve B stainless steel, prebent LC216
4 Valve A to flow sensor A PEEKsil, 50 μm ID, 25 cm length LC222
Valve B to flow sensor B
5 Flow sensor A to mixing Tee PEEKsil, 20 μm ID, 21 cm length Kit LC243
6 Flow sensor B to mixing Tee Fused silica, 10 μm ID, 15 cm length
7 Mixing Tee to valve S PEEKsil, 30 μm ID, 13 cm length
8 Autosampler needle connected to port 1 of valve S PEEKsil, 150 μm ID, 55 cm length
ASA model LC251
ASC model LC302
9 Column Out tubing connected to port 3 of valve S PEEKsil, 30 μm ID, 37 cm length LC260
10 Waste In line, venting Tee to port 2 of valve W PEEKsil, 75 μm ID, 50 cm length LC262
11 Port 2 of valve A to check valve A Teflon, 500 μm ID, 15 cm length Kit,
Port 2 of valve B to check valve B Low-pressure
12 Tubing from check valve A to solvent bottle A Teflon, 500 μm ID, 37 cm length solvent lines
Tubing from check valve B to solvent bottle B LC230
13 Tubing from check valve A to the waste beaker Teflon, 500 μm ID, 39 cm length
Tubing from check valve B to the waste beaker
14 Tubing from valve W to the waste beaker Teflon, 500 μm ID, 27 cm length LC263

Figure 259. Solvent system schematic for the EASY-nLC II system
12 12
Solvent A Solvent B
13
Check valves
for solvent A
13
Check valves
for solvent B
10 11
11
4
2
1
6 2
1
6 2
1
6 2
1
6 4
W S A B
Flow
↓ ↓ sensor
B
Flow sensor A
9 5
6
14 7 Mixing Tee
Waste
1 1 3
Pressure sensor Pressure sensor Pressure sensor
PEEK
1 1 2
Stainless steel
PEEKsil
Teﬂon
Fused silica
Pump S Pump A Pump B

Solvent System Schematic for the EASY-nLC 1000 Instrument

The pump and valve compartment behind the right panel of the EASY-nLC instrument
contains all the flow lines between the components. In addition to pumps and valves, the
solvent delivery and waste system includes several filters and four check valves. The two check
valves on each solvent line ensure that solvent is drawn from the solvent bottles and ejected to
waste without switching valve positions.
Table 33 lists the tubing requirements and identifies the tubing components shown in
Figure 260. The Low-Pressure Solvent Line Kit (P/N LC230) contains the Tees, check valves,
and low-pressure solvent lines to connect one pump (A or B) to the waste system and to its
corresponding solvent bottle and six-port rotary valve. The EASY-nLC 1000 Flow Line Kit
(P/N LC570) contains all of these flow lines. The stainless steel tubing is prebent.
Table 33. Tubing requirements for the EASY-nLC 1000 system
No. Connections Tubing Part number
1 Pump outlet to pressure sensor inlet Stainless steel, 250 μm ID, 150 mm length LC512
2 Pressure sensor outlet to valve A or B Stainless steel, 250 μm ID, 150 mm length LC513
3 Pressure sensor outlet to valve S Stainless steel, 250 μm ID, 150 mm length LC514
4 Mixing Tee to valve S, nanoViper, 20 μm ID, 350 mm length LC522
valve A to flow sensor A,
valve B to flow sensor B,
flow sensor A to mixing Tee
5 Flow sensor B to mixing Tee nanoViper, 10 μm ID, 180 mm length LC543
6 Autosampler needle connected to port 1 of PEEKsil™, 150 μm ID, 550 mm length LC302
valve S
7 Column Out tubing connected to port 3 of nanoViper, 20 μm ID, 550 mm length LC560
valve S
8 Waste In line, venting Tee to port 2 of nanoViper, 75 μm ID, 550 mm length LC562
valve W
9 Sample loop, 20 μL nanoViper, 250 μm ID, 410 mm length LC472
D Port 2 of valve A to check valve A Teflon™, 500 μm ID, 150 mm length kit LC230
Port 2 of valve B to check valve B
E Tubing (2) from check valves to solvent Teflon, 500 μm ID, 390 mm length kit LC230
bottles
F Tubing (2) from check valves to waste beaker Teflon, 500 μm ID, 390 mm length kit LC230
G Tubing from valve W to waste beaker Teflon, 500 μm ID, 330 mm length LC263

Figure 260. Solvent system schematic for the EASY-nLC 1000 system
E E
Solvent A Solvent B
F
F
8
D D
9
1 1 1
4 1 4
2 6 2 6 2 6 2 6
S W A B
↓ ↓
7
4
G 2 5
3
4 2
Pressure sensor Pressure sensor Pressure sensor
1 1 1
Waste

Common Replacement Parts

For proper maintenance of your EASY-nLC instrument, Thermo Fisher Scientific
recommends that you maintain an inventory of replacement parts.
• Common Replacement Parts for the EASY-nLC II Instrument
• Common Replacement Parts for the EASY-nLC 1000 Instrument
Common Replacement Parts for the EASY-nLC II Instrument

Table 34 lists the annual consumption of common replacements parts for the
Table 34. Common replacement parts for the EASY-nLC II instrument
Description Part number Quantity
Pump Piston Seal LC210 4 piston seals (1 per pump) +
Replacement Kit (contains 1 extra
four piston seals and the
piston seal tool)
Valve rotor seal for valve LC224 8 rotor seals (2 per valve)
serial numbers V-009999
and below (contains one
rotor seal)
Valve rotor seal for valve LC228 8 rotor seals (2 per valve)
serial numbers V-010000
and above (contains one
rotor seal)
Column Out solvent line LC260 2
Waste In solvent line LC262 1
Autosampler needle, ASA LC251 1
model
Autosampler needle, ASC LC302 2
model
Valve to flow sensor line LC222 2
(contains two flow sensor
lines)
Replacement filter discs LC232 2 filter discs (1 per solvent
(contains two 10 μm filter bottle)
discs)

Common Replacement Parts for the EASY-nLC 1000 Instrument

Table 35 lists the annual consumption of common replacements parts for the
Table 35. Common replacement parts for the EASY-nLC 1000 instrument
Description Part number Quantity
Pump Piston Seal LC510 4 piston seals
Replacement Kit (contains (1 per pump) + 1 extra
four spring-energized piston
seals and the piston seal tool)
Valve rotor seal LC228 8 rotor seals (2 per valve)
(contains one rotor seal)
Column Out solvent line LC560 2
Waste In solvent line LC562 1
Autosampler needle, ASC LC302 2
model
Flow sensor filters (contains LC542 4 flow sensor filters
four flow sensor filters) (2 per flow sensor)

D
Quick Reference Guides for Routine Maintenance

This appendix contains a set of quick reference guides for the routine maintenance procedures
that you can perform to keep the EASY-nLC system in optimal working condition. These
guides are the condensed versions of the procedures in the Routine Maintenance chapter.
If you have replaced a PLF pump in the EASY-nLC II instrument with a PLU pump, follow
the instructions in “Maintaining the PLU Pump Quick Reference Guide” on page 327 to
maintain the new PLU pump.
Contents
• Using nanoViper Fittings Quick Reference Guide
• Maintaining the PLU Pump Quick Reference Guide
• Maintaining the PLF Pump Quick Reference Guide
• Maintaining the Rotary Valves Quick Reference Guide
• Replacing a Damaged Autosampler Needle
Thermo Scientific manual-name 321

Using nanoViper Fittings Quick Reference Guide
For the EASY-nLC 1000 instrument, most of the plumbing connections use nanoViper fittings (see Figure 1).
Figure 1. nanoViper fitting
PEEK
sealing Screw
surface Removable knurled nut
Even though nanoViper fittings can withstand UHPLC back pressures of up to ~1034 bar (~15 000 psi), they are
fingertight fittings, which require only very small torques to seal. To avoid damage by overtightening, follow the
instructions in this guide.
Contents
• Connecting nanoViper Fittings

• nanoViper Tubing Connections
• Returning the System to Atmospheric Pressure
Connecting  To connect a nanoViper fitting to a receiving port

nanoViper 1. Insert the nanoViper fitting into the receiving port. Then turn the screw clockwise until you feel resistance.
Fittings 2. Using the black knurled nut, turn the screw clockwise to an angle between 0 and 45 degrees (1/8-turn).
3. Run the system leak test (see “Running a System Leak Test” on page 218).
When the leak test ends, the system is at atmospheric pressure.
IMPORTANT To extend the lifetime of the nanoViper fittings, open and close connections at atmospheric
system pressures only. Opening and closing connections at high system pressures can reduce the lifetime of
the fitting system.
4. If the Leaks script fails because the new connection is not leak tight, use the black knurled nut to turn the screw
up to an additional 45 degrees. Do not turn the screw beyond an angle of 90 degrees from where you felt the
initial resistance.
IMPORTANT To prevent damage to the sealing surface of the nanoViper fitting, take care not to overtighten
the fingertight nanoViper fitting.
© 2012 Thermo Fisher Scientific Inc.

All rights reserved.
nanoViper Figure 2 shows the nanoViper tubing connections in the EASY-nLC 1000 instrument.
Tubing • Port 6 of valve A to flow sensor A inlet
Connections • Port 6 of valve B to flow sensor B inlet
• Flow sensor A outlet to mixing Tee inlet
• Flow sensor B outlet to mixing Tee inlet
• Mixing Tee outlet to port 4 of valve S
• Sample loop connected to ports 2 and 5 of valve S
• Column Out line connected to port 3 of valve S and the HPLC union
• Waste In line connected to port 2 of valve W and the HPLC union or the venting Tee
Figure 2. nanoViper tubing connections in the EASY-nLC 1000 instrument
Valve A Column Out line
2 6
Valve S
1
Sample loop 2 6
Flow sensor A ↓
Mixing Tee
Flow
3 5
4
VICI
Valve B
2 6 Waste In line
Flow
Valve W
2 6
Flow sensor B ↓
324
Returning Before you disconnect a nanoViper fitting from its receiving port, always return the solvent line to atmospheric
the System to pressure. The high-pressure solvent lines in the EASY-nLC solvent system can be divided into two categories based
on their position relative to valve S.
Atmospheric
• Upstream of Valve S Solvent Lines
Pressure
• Downstream of Valve S Solvent Lines
Upstream of The following solvent lines (numbered from left to right in Figure 3) are in the flow path upstream of valve S.
Valve S
# Solvent line # Solvent line
Solvent Lines
1 Port 6 of valve A to flow sensor A inlet 4 Flow sensor B outlet to mixing Tee inlet
2 Port 6 of valve B to flow sensor B inlet 5 Mixing Tee outlet to port 4 of valve S
3 Flow sensor A outlet to mixing Tee inlet 6 Sample loop connected to ports 2 and 5 of valve S
 To return the solvent lines that are upstream of valve S to atmospheric pressure
1. On the touch screen, press Home > Overview.
2. Using the valve controls, set the valves to the following positions.
Valve Position Effect

A and B Center Maintains the pressure between the pump A and valve A during the
Analytical Column Equilibration script.
S and W 1–6 Vents the system pressure downstream of valve A.
Figure 3 shows the flow path when valves A and B are Centered and valves S and W are in position 1–6.
Figure 3. Solvent lines that are downstream of valves A and B and upstream of valve S, numbered 1–6
No flow 1
6
1 2
3
S
6
5
↓
1
2
3
A
6
5
3 Mixing Tee
4
5
Center position
No flow
2
↓
2
1
B
6 4
3 5
4
Center position
1
2 6
3
W5
4
Waste beaker
325
Downstream of The following solvent line connections are in the flow path downstream of valve S:
Valve S • Column Out tubing connected to port 3 of valve S and the HPLC union (P/N SC900)
Solvent Lines • Waste In tubing connected to port 2 of valve W and the HPLC union or the venting Tee
 To return the solvent lines that are downstream of valve S to atmospheric pressure
1. On the touch screen, press Home > Overview.
2. Using the valve controls, set the valves to the following positions.
Valve Position Effect

S Center Maintains the system pressure upstream of valve S.
W 1–6 Vents the system pressure downstream of valve S.
Figure 4 shows the Column Out and Waste In solvent lines that are downstream of valve S.
Figure 4. Solvent lines that are downstream of valve S
1
2 6
3
S 5
4
Column Out
line
Waste In
line
1
2 6
3
W5
4
Waste beaker
326
Maintaining the PLU Pump Quick Reference Guide
Replace the piston seal when you detect a leak in the pump. 2. Exit the EASY-nLC 1000 system and turn off the power.
3. Using a #2 Phillips head screwdriver, with a quarter-turn loosen
Contents
the three captive screws that secure the right side panel to the
• Removing a Used Piston Seal instrument. Then remove the panel.
• Installing a New Piston Seal
CAUTION Wear powder-free gloves when handling
Replacing a piston seal requires these tools and materials. the wetted components of the LC system.
Tools Materials 4. Remove the used piston seal as follows:

3 mm hex wrench Pipette a. Using a 1/4 in. open-ended wrench, remove the stainless steel
Piston seal tool Powder-free safety gloves tubing connected to the pump head.
Figure 2. Stainless steel fitting removed from the pump head
1/4 in. open-ended wrench LC/MS-grade methanol
#2 Phillips head screwdriver LC/MS-grade acetonitrile Stainless steel tubing
Piston seal, P/N LC510
Removing a Used Piston Seal

1. Set the pump piston to the fully retracted position as follows:
e. Press Purge Iterations and enter 0. b. Using a 3 mm hex wrench, remove the two screws that secure
Figure 1. Purge Solvent script set to 0 iterations the pump head to the pump body.
Figure 3. Pump head removed from the pump body
f. Select the check box for the appropriate pump. c. Clean the visible portion of the piston with a lint-free tissue
g. Press Start. soaked in LC/MS-grade methanol and visually inspect the
piston for scratches. Ensure that no solvent runs into the
The piston moves downward to the 140 μL position.
pump.
d. Remove the old seal from the pump head with great care. Do
not use any metal tools, as they can scratch the inside of the
pump head and generate leaks.
Installing a New Piston Seal d. Pipette the appropriate solvent into the pump head.
1. With the spring side of the piston seal spring facing away from Figure 7. Adding solvent to the pump head
the piston seal tool, mount the new piston seal onto the piston
seal tool.
2. Using a pipette, remove the air from the piston seal spring by
carefully filling the rim of the piston seal with methanol.
Figure 4. Filling the piston seal with methanol
e. Set flow rate to –300 μL/min and the volume to 140 μL.
Then press Start.
The piston moves down, drawing solvent into the pump
head. Make sure the pump head is filled with solvent during
the entire retraction of the piston.
3. Place the pump house on the guide rods and evenly press it all the
way down to insert the seal and then gently remove the house CAUTION Be careful not to spill solvent onto
when the seal is in position. the printed circuit board behind the LED panel.
Figure 5. Inserting the piston seal into the pump head
7. Using a 1/4 in. open-ended wrench, reconnect the tubing to the
pump head (see Figure 2 on page 327).
8. Reinstall the right side panel.
9. Reset the usage counter for the pump as follows:
b. Select the pump from the list of devices.
4. Reassemble the pump head on the pump using the two screws d. Press Reset.
and a 3 mm hex wrench. Do not connect the stainless steel tubing
to the pump head. The value in the Intermediate Volume box resets to 0.
5. Turn on the EASY-nLC system and log in as an administrator. 10. To draw fresh solvent through the solvent lines and to remove air,
do the following:
6. Fill the pump head with the appropriate solvent as follows:
a. Open the Parameters page for the Purge Solvent script as
described in step 1 on page 327.
b. In the Purge Iterations box, enter 10.
The Position readback displays the current pump position c. Select the check box for the appropriate pump.
from 0 μL (empty) to 140 μL (full).
d. Press Start and wait for the system to perform 10 purge
c. Set the flow rate to 300 μL/min and the volume to 140 μL. cycles.
Then press Start.
11. To remove air from the pump head, do the following:
The piston moves up to the top of the pump head.
a. In the Name category on the Maintenance > Scripts page,
Figure 6. Pump dialog box select Flush Air.
c. In the Flush Threshold [μL] box, enter 12.
d. Press Start.
12. Run the Leaks script for the pump with the new piston seal
a. On the Maintenance > Scripts page, select Test in the
Category list, and then select Leaks in the Name list.
c. Select the check box for the pump with the new seal.
d. Press Start.
13. . When the instrument is leak tight, it is ready for use.
328
Maintaining the PLF Pump Quick Reference Guide
Replace the piston seal when you detect a leak in the pump.
• If a stainless steel fitting is connected to the pump head, use a
Contents 1/4 in. open-ended wrench to remove it.
Figure 2. Stainless steel fitting on the internally threaded pump head
1. Removing the Pump Head and Cleaning the Piston
2. Removing the Worn Piston Seal Stainless steel fitting
3. Installing a New Piston Seal connected to an internally
threaded pump head
4. Priming the Pump
5. Preparing the Instrument for Operation
5. Using a 13 mm open-ended wrench, remove the pump head.

CAUTION Wear powder-free safety gloves when Figure 3. Removing the pump head
working with solvents and handling the wetted
components of the instrument.
Pump head
Replacing a piston seal requires these tools and materials.
Tools Materials
3 mm hex wrench Pipette
6. Place the piston in the fully extended position as follows:
Piston seal tool Powder-free safety gloves a. Turn on the instrument and log in as an administrator.
1/4 in. open-ended wrench LC/MS-grade methanol b. Press Home > Overview, and then press the pump icon for
#2 Phillips head screwdriver LC/MS-grade acetonitrile the pump you want to control. The Pump dialog box opens.
Piston seal, P/N LC210 (includes c. Set the flow rate to 300 μL/min and the volume to 140 μL.
the piston seal tool) d. Press Start.
7. Clean the piston with the lint-free tissue soaked in methanol, and
Removing the Pump Head and Cleaning the Piston
visually inspect the piston for any scratches.
1. Set the pump piston to the fully retracted position as follows:
a. On the Maintenance > Scripts page, Select Prepare in the CAUTION Take care to avoid solvent drips onto the
Category list and then select Purge Solvent in the Name list. pump PCB.
Press the Parameters tab. In the Purge Iterations box, enter 0.
Select the check box for the appropriate pump.
8. Return the piston to the fully retracted position as follows:
b. Press Start. The piston moves down to the 140 μL position.
a. In the Pump dialog box, set the flow rate to – 300 μL/min
2. Exit the EASY-nLC II system and turn off the power. and the dispense volume to 140 μL.
3. Using a #2 Phillips head screwdriver, with a quarter-turn loosen b. Press Start.
the three captive screws that secure the right side panel to the
instrument. Then remove the panel. 9. When the piston is fully retracted, close down the EASY-nLC
system and turn off the power.
4. Remove the tubing connected to the pump head as follows:
• If a PEEK fitting is connected to the pump head, use a
13 mm open-ended wrench, to remove it.
Figure 1. PEEK fitting on the externally threaded pump head
PEEK fitting connected to an

externally threaded pump head
Removing the Worn Piston Seal Priming the Pump
1. Clean the piston seal tool in a beaker filled with 100% methanol. 1. Turn on the EASY-nLC instrument and log in as an
Figure 4. Two-component piston seal tool for the PLF model pump administrator.
2. Fill the pump head with the appropriate solvent as follows:
c. Set the flow rate to 300 μL/min and the volume to 140 μL.
Then press Start.
The piston moves upward to the top of the pump head.
2. Insert the piston seal tool into the worn piston seal and pull the d. Pipette the appropriate solvent into the pump head.
piston seal out of the pump head.
e. Set the flow rate to –300 μL/min and the volume to 140 μL.
Figure 5. Using the piston seal tool to remove the worn piston seal Then press Start.
The piston moves down, drawing solvent into the pump
head. Make sure the pump head is filled with solvent during
Worn piston seal the entire retraction of the piston.
CAUTION Be careful not to spill solvent onto

the printed circuit board behind the LED panel.
3. Using a 1/4 in. open-ended wrench, reconnect the tubing to the

Installing a New Piston Seal pump head.
1. Insert the guide tube into the pump head flange.
Figure 6. Guide tool inserted into the pump head flange Preparing the Instrument for Operation
1. Reinstall the right panel.
Guide tool
2. Reset the usage counter for the pump as follows:
b. Select the pump from the list of devices.
2. Using a pipette, fill the groove in the piston seal with methanol. c. Press the Summary tab.
3. Place the new seal with the groove facing up on the piston seal d. Press Reset.
tool. The value in the Intermediate Volume box resets to 0.
Figure 7. Piston seal mounted onto the piston seal tool 3. To draw fresh solvent through the solvent lines and to remove air,
do the following:
a. Open the Parameter page for the Purge Solvent script.
b. In the Purge Iterations box, enter 10.
c. Select the check box for the appropriate pump.
d. Press Start and wait for the system to perform 10 purge
cycles.
4. Insert the piston seal tool into the guide tool. 4. To flush air from the pump head, do the following:
Figure 8. Inserting the piston seal tool into the guide a. In the Name category on the Maintenance > Scripts page,
select Flush Air.
c. In the Flush Threshold [μL] box, enter 10.
d. Press Start.
5. Run the Leaks script for the pump as follows:
a. On the Maintenance > Scripts page, select Test in the
5. Push the piston seal tool into the guide until you feel resistance. Category list, and then select Leaks in the Name list.
6. Remove the guide tube and the piston seal tool, and then check b. Press the Parameters tab.
that the piston seal is properly seated.
c. Select the check box for the pump with the new seal.
7. Using a 13 mm open-ended wrench, reconnect the pump head to
d. Press Start.
the pump body. Do not connect the stainless steel tubing to the
pump head. 6. When the instrument is leak tight, it is ready for use.
330
Maintaining the Rotary Valves Quick Reference Guide
Replace the rotor seal when you detect a leak or blockage in the valve. Figure 2. Cleaning the stator
T
Contents
• Replacing a Rotor Seal

• Replacing the Stator
CAUTION Wear powder-free safety gloves when

working with solvents and handling the wetted
components of the instrument. 6. Carefully mount the new rotor onto the valve driver, ensuring
that the rotor sealing surface (engraved flow passage), is facing
Replacing a piston seal requires these tools and materials. out.
Tools Materials 7. Mount the stator onto the valve driver.
• 9/64 in. hex wrench • Rotor seal, P/N LC228 8. Using a 9/64 in. L-hex wrench, tighten the two hex screws a little
(EASY-nLC system valves with at a time by shifting from one screw to the other and back again
• 1/4 in. open-ended until the screws are evenly torqued.
wrench serial numbers V-010000 and
above) 9. Reconnect the right side panel.
• #2 Phillips head • Rotor seal, P/N LC224 10. Turn on the EASY-nLC instrument and log in as an
screwdriver (EASY-nLC II system valves with administrator.
serial numbers below V-009999) 11. Reset the usage counter for the valve as follows:
• LC/MS-grade methanol a. Press Maintenance > Devices.
• Powder-free safety gloves b. Select the valve from the list of devices.
Replacing a Rotor Seal
d. Press Reset.
1. Close down the EASY-nLC system, and then turn off the power
to the instrument. The value in the Rotor Shifts box resets to 0.
2. Using a #2 Phillips screwdriver, with a quarter-turn loosen the 12. If you replaced the rotor seal in Valve A or B, flush air from the
three captive screws that secure the panel to the right side of the system as follows:
EASY-nLC instrument, and then remove the panel. a. On the Maintenance > Scripts page, select Prepare in the
3. Using a 9/64 in. L-hex wrench, remove the two hex screws that Category list. Then select Flush Air in the Name list.
secure the stator to the valve assembly, and then pull the stator b. Select the pump that is connected to the affected valve.
away from the valve driver. c. Set the flush volume threshold to 10 μL for the EASY-nLC II
4. Remove the rotor seal from the valve driver. or 12 μL for the EASY-nLC 1000.
Figure 1. Rotor seal mounted on the valve driver d. Press Start.
13. Run the Leaks script as follows:
a. Select Test in the Category list. Then select Leaks in the
Name list.
b. Do one of the following:
• If you replaced the rotor seal in Valve A or B, run the
Leaks script for the affected valve.
5. Clean the stator with a lint-free tissue or Q-tip soaked in • If you replaced the rotor seal in Valve S or W, run the
methanol. Leaks script for the system.
When the system is leak tight, the instrument is ready for use.
Replacing the Stator
1. Close down the EASY-nLC system, and then turn off the power
to the instrument (see “Closing Down the EASY-nLC
Instrument” on page 21).
2. Using a #2 Phillips screwdriver, loosen the three quarter-turn
screws that secure the panel to the right side the EASY-nLC
instrument, and then remove the panel.
3. Disconnect the solvent lines from the valve as follows:
• Use a 1/4 in. open-ended wrench to remove stainless steel
fittings.
• Use the black nanoViper knurled nut to remove nanoViper
fittings.
4. Using a 9/64 in. L-hex wrench, remove the two hex screws that
secure the stator to the valve driver, and then pull the stator away
from the valve driver.
5. Mount the new stator onto the valve driver.
6. Using a 9/64 in. L-hex wrench, tighten the two hex screws a little
at a time by shifting from one screw to the other and back again
until the screws are evenly torqued.
7. Reconnect the solvent lines to the valve as follows:
• Use a 1/4 in. open-ended wrench to tighten stainless steel
fittings.
• Use the black nanoViper knurled nut to tighten nanoViper
fittings.
8. Reconnect the right side panel to the instrument. Tighten the
three screws with a #2 Phillips screwdriver.
9. Turn on the EASY-nLC instrument and log in as an
administrator.
10. If you replaced the stator in Valve A or B, run the Flush Air script
for the valve with the replacement stator.
11. If you replaced the stator on Valve A or B, run the Leaks script for
the valve with the replacement stator. If you replaced the stator on
Valve S or W, run the Leaks script for the system.
332
Replacing a Damaged Autosampler Needle
Replace the autosampler needle when it is bent or clogged. Figure 2. Valve S solvent line connections for the EASY-nLC 1000 system
T
Contents 1 From the

Autosampler 6 pressure
• Removing the Damaged Autosampler Needle 2
needle sensor
• Installing a New Autosampler Needle
5
3
CAUTION Wear powder-free safety gloves when
working with solvents and handling the wetted 4
Column Out line
components of the instrument.
From the
Replacing a damaged needle requires these tools and materials. mixing Tee
Tools Materials
3. Remove the nut, ferrule, and sleeve from the needle tubing.
Figure 3. Autosampler tubing with a nut, ferrule, and sleeve at one end
• #2 Phillips head screwdriver • ASA autosampler needle,
P/N LC251
• ASC autosampler needle,
P/N LC302
4. Move the z-axis needle holder to an accessible location within the
Removing the Damaged Autosampler Needle tray compartment by doing one of the following:
 To remove the autosampler needle • For the ASA model, go to step 5.
1. Using a #2 Phillips screwdriver, with a quarter-turn loosen the • For the ASC model, go to step 6.
three captive screws that secure the panel to the right side the 5. For the ASA model, move the z-axis needle holder to position A1
EASY-nLC instrument, and then remove the panel. as follows:
2. Using a 1/4 in. open-ended wrench, unscrew the nut that secures a. Press Home > Overview.
the autosampler needle to port 1 of valve S. Then remove the
b. Press the autosampler icon.
fitting from the port.
c. The Autosampler dialog box opens.
Figure 1. Valve S solvent line connections for the EASY-nLC II system
d. In the XYZ Robot area, select position A1 in the Well box.
Figure 4. Autosampler direct control dialog box
Valve S
Autosampler 1
needle
1
2 6
6
2
3 5
5
3
4
Column Out
line 4 From the
pressure
From the sensor
mixing Tee
e. Press Goto.
f. Go to step 7.
6. For the ASC model, move the z-axis needle holder to Figure 7. Autosampler needle connected to the z-axis needle holder
position W1 as follows: ASA z-axis needle holder ASC z-axis needle holder
b. Press the autosampler icon.
c. In the XYZ Robot area, press Go to Calibration.
The Tools page of the Autosampler view on the
Maintenance > Devices page opens.
Figure 5. Tools page of the Autosampler view on the Maintenance >
Devices page
Installing a New Autosampler Needle

 To install an new autosampler needle
1. Mount the new autosampler needle in the z-axis holder. Check
that the small spring is situated between the PEEK nut and the
plastic stop.
• For the ASC autosampler, go to step step 3.
d. In the Manipulator area, press Reset.
• For the ASA autosampler, go to step step 4.
The z-axis needle holder moves to the W1 position.
3. For the ASC autosampler, do the following:
7. Using a #2 Phillips screwdriver, loosen the three quarter-turn
a. Guide the end of the needle that connects to Valve S through
screws that secure the panel to the left side of the EASY-nLC
the large hole in the metal plate that separates the tray
instrument, and then remove the panel.
compartment from the solvent system compartment.
b. Install the black needle holder in the side plate.
• For the ASC model, remove the black needle holder from the 4. For the ASA autosampler, slide the valve end of the tubing
slot in the panel that separates the solvent system hardware through the small plastic holder on the back of the touch-screen
from the autosampler compartment. Removing the fitting monitor.
requires some gentle movement from both sides of the plate.
Figure 8. Holder on the back of the touch-screen monitor
Figure 6. Removing the black needle holder from the slot in the panel
Black needle Slot in the

holder metal plate
Holder
5. Connect the needle to port 1 of Valve S as follows:

a. Slide the provided blue sleeve and metal fittings onto the
tubing.
b. To ensure a zero dead volume connection, hold the blue
sleeve and the tubing firmly against the bottom of the valve
port, and then tighten the fitting with a 1/4 in. open-ended
wrench.
6. Recalibrate the needle position.
• For the ASA model, remove the white plastic needle guide on 7. Press Maintenance > Scripts.
the back of the touch-screen monitor. 8. In the Category list, select Prepare.
9. Loosen the nut that is connected to the z-axis needle holder by 9. In the Name list, select Purge Solvent. Then run 2 iterations of
turning it counterclockwise. Then carefully pull the autosampler the Purge Solvent script for Pump S.
needle upward and away from the holder. 10. In the Name list, select Flush Air. Then run the Flush Air script
for Pump S with a flush volume threshold of 10 μL for the
EASY-nLC II system or 12 μL for the EASY-nLC 1000 system.
334
I
Index
A B
Acquisition Server errors 189 back panel, instrument 16
adapter plate, replacing back pressure
ASA autosampler 272 testing 48
ASC autosampler 271 troubleshooting
air, removing from pump heads 33 maximum pressure spikes during gradient 180
Analytical Column Equilibration script 36 system blockage 249
application version 20 too high during sample loading and column
ASA autosampler equilibration 178
adapter plate, replacing 272 Back Pressure script 48
description 4 backup ring 8
needle, description of 14 beaker, waste 2
See also blank injections, troubleshooting 183–184, 263
autosampler blind fitting, EASY-nLC 1000 instrument 218
upgrading to ASC autosampler (service repair) 128 blockage, troubleshooting 249
ASA cooler, replacing (service repair) 140
ASC autosampler C
adapter plate, replacing 271
cables, internal
description 3 connected to EASY-nLC 1000 pump 152
needle, description of 14 cooler bus cable 123
replacing (service repair) 122 LVDS cable 108, 114, 116
See also monitor cable 114
autosampler
P-Bus communication cables 118, 158
ASC cooler, replacing (service repair) 137 PC box cable connections 108
autosampler pressure sensor communication cable 119
calibrating XYZ robot 269–286 USB cable 114
checking sample pickup, schedule 28 calibrating
description 2 autosampler XYZ robot 269–286
direct control 210 flow sensors 51
needle plates 280
blocked 262 pressure sensors 52
description 14
carryover
replacing 84–88
specification 23
Sample Pickup script 263
troubleshooting tips 194
Torque script 49
check valves
tray compartment, accessing 2
description 11
troubleshooting tips 171
replacing 80

Index: D
checking EASY-nLC II instrument (service repairs)

check valves for leaks 29, 248 ASA cooler, replacing 140–146
sample pickup 263 ASC autosampler, replacing 122–127
solvent levels 27 ASC cooler, replacing 137–139
system for leaks 44 autosampler, upgrading ASA to ASC 128–136
clogged column or system, troubleshooting 178 monitor, replacing 113–116
closing down the EASY-nLC instrument 21 PC box, replacing 108–112
Column Out line PLF pump, replacing 154
checking for blockage 253 pressure sensor, replacing 117–121
clogged 178, 180 pump PCB, replacing 167–168
tubing ID 249 electromagnetic compatibility iii
column, clogged 178 Exit button 21
compliance
FCC iii F
regulatory iii failure messages 216
WEEE ix fan cables 145
compliance, electromagnetic v, vii Fast Inspection option 52
computer, integrated FCC compliance iii
location 15 field service repairs
out of memory 202 See
PC box, replacing (service repair) 108 EASY-nLC II instrument or EASY-nLC 1000
consumables 318 instrument (service repairs)
contact closure filling a pump with solvent 206
MS Connection script 39 flow rate
troubleshooting 172 determining appropriate
contamination analytical column 36
declaration 301 precolumn 34
preventing 205 direct control 205
cooler PCB 132 measuring 10
cooler temperature flow sensor cable 152, 163, 166
checking 28 flow sensors
direct control 211 calibration script 51
checking for blockage 255, 259
D description 10
daily maintenance 27 maintenance schedule 29
Declaration of Conformity v, vii replacing
Declaration of Contamination 301 EASY-nLC 1000 instrument 92
EASY-nLC II instrument 96
devices
managing the Devices list 105 Flush Air script 33
usage counters 56 fuse, replacing 58
Direct Infusion script 53
G
E grounding requirements 268
EASY-nLC 1000 instrument (service repairs)
ASC autosampler, replacing 122–127 H
ASC cooler, replacing 137–139 hard drive, replacing 100
high-pressure valves, replacing 147–149 HPLC union 218
monitor, replacing 113–116
PC box, replacing 108–112
PLU pump, replacing 150–153
pump PCB, replacing 163–166

Index: I
I P
inline filters, replacing in the EASY-nLC 1000 instrument 81 parts, common replacement 318
Inspection Only check box 52 password, initial 20
instrument startup, troubleshooting 172 P-Bus communication cables
interface layout 19 connecting to cooler PCB 132, 139
IP address, support server 289 connecting to pump 166
Isocratic Flow script 38 connecting to pump PCB 121, 168
connecting to XYZ-axis PCB 132
L disconnecting from cooler PCB 129, 137
disconnecting from pump 152, 163
L brackets, pressure sensor 91, 120, 157 disconnecting from pump PCB 118, 158, 167
Leaks script 44–46 disconnecting from XYZ-axis PCB 129
leaks, checking for 28, 44–46, 218–247 inserting P-Bus connector 131
log book 55 PCBs connected to 132
Logo icon, Thermo Scientific 20 P-Bus connector 131
loop, sample, replacing 89 PC box
lower case letters, cause of Acquisition Server error 189 cables connected to 108
low-pressure solvent filters 29 replacing (service repair) 108
LVDS cable, internal 114, 116 Terminated label 131
PCB shield 164, 166
M performance specifications 23
maintenance pink
daily 27 autosampler icon 201
quarterly 28 pump icons 199
scripts 31 valve icon 200
weekly 28 piston seals
yearly 29 function 8
manuals, EASY-nLC xx replacing
in the PLF model pump 62
mass spectrometer, contact closure
in the PLU model pump 67
MS Connection script 39
troubleshooting 172, 266 plate formats
creating 275
memory stick, correct format 202
deleting 277
message.log file 292
selecting 274
messages, failure 216
plates, calibrating 280
mixing Tee
plug, EASY-nLC II instrument 218
checking for blockage 254
port 22, firewall setup for 287–288
installing in the EASY-nLC II instrument 135
Power Down button 22
monitor cable, internal 114
monitor, replacing (service repair) 113 power, turning off 22
preparing
motor cable 165–168
autosampler for the calibration routines 278
MS Connection script 39
system for daily use 27
pressure sensor cable 152, 163, 166
N pressure sensors
nanoViper fittings communication cable 119, 121, 167
EASY-nLC 1000 solvent lines 316 description 10
using 83, 323 grounding cable
needle arm 135 connecting to PCB (service repair) 118, 121, 168
needle guide, white plastic 115–116 replacing
needle position, calibrating 278–286 EASY-nLC 1000 instrument
needle, autosampler 14 (routine maintenance) 90
network access, troubleshooting 264 EASY-nLC II instrument (service repair) 117

Index: Q
pump scripts
direct control 205 Analytical Col Equilibration 36
manual control 71, 205 Autosampler Torque 49
PLF, EASY-nLC II instrument Back Pressure 48
description 8 Flow Sensors 51
maintaining 62 Flush Air 33
replacing (service repair) 154 Isocratic Flow 38
PLU, EASY-nLC 1000 instrument Leaks 44
description 8 Maintenance 31
maintaining 67 MS Connection 39
replacing (service repair) 150 Purge Solvent 32
volume pumped usage counter 56 Reset Pressure Sensor 52
Pump dialog box 206 Sample Pickup 42, 263
Pump Mounting Kit 154, 160 Valve Check 47
pump PCB, replacing (service repair) Valve Tune 50
EASY-nLC 1000 instrument 163–166 seals
EASY-nLC II instrument 167–168 piston
Purge Solvent script 32 description 8
replacing
Q in the PLF model pump 62
in the PLU model pump 67
quick reference guides
Secure Shell (SSH) network protocol 287
autosampler needle, replacing 333
serial numbers, device 106
EASY-nLC 1000 pump, maintaining 327
EASY-nLC II pump, maintaining 329 service log 55
nanoViper fittings, using 323 service repairs
valves, maintaining 331 See
EASY-nLC II instrument or EASY-nLC 1000
instrument (service repairs)
R
sharp objects, autosampler needle 278
regulatory compliance iii
sluggish system operation 202
remote support 287
software, upgrading the touch-screen application 128, 296
replacement parts, common 318 solvent system
Reset Pressure Sensor script 52 components behind the right side panel 5
rotary valves schematic
See EASY-nLC 1000 system 317
valves EASY-nLC II system 315
rotor seal, replacing 77 solvents
checking levels 27
S viscosity table 311
safety specifications
calibrating the autosampler 278 performance 23
precautions for the EASY-nLC instrument xxi technical 24
standards (EMC) vii spray, unstable 196
safety standards iii SSH Connection Error message box 292
safety standards (EMC) v stator
sample cleaning 75
pickup check 263 replacing 79
Pickup script 42 support collar 148
sample loop, replacing 89 support server, IP address 289
schedule, maintenance 27 swept volume, extra 176
system overload 202

Index: T
T valves
check valves
technical specifications 24
description 11
technical support, contacting xxiii
replacing 80
Telnet window 266 checking for blockage
temperature valve B 257
direct control 211 valves A, S, and W 251
maintaining stable 284 checking for leaks
Terminated label, PC box 131 valve B 223
touch-screen software rotary
description 18 description 12
upgrading 128, 296 maintaining 74
transport instructions 299 replacing 147
tray compartment, accessing 2 versions, application 20, 297
troubleshooting vials
autosampler 171 extra vial positions, calibrating 285
contact closure 172 plate format, calibrating 280
identifying and locating leaks 218 viscosities, solvent 311
instrument startup 172
network access 264 W
system blockage 249
wash bottles
turning off the EASY-nLC instrument 21 calibrating W4 bottle with insert 285
description 2
U waste beaker, description 2
union, HPLC 218 Waste In line
upgrading the touch-screen software 128, 296 checking for blockage 253
URLs weak signal from detector 183
consumable parts xxiii WEEE compliance ix
customer manuals xx weight, EASY-nLC instrument 25
usage counters, device 56 well plates
USB cable, internal 114 calibrating 280
USB ports, EASY-nLC instrument 17, 293 plate formats, managing 274
USB storage device, copying system files 293
user interface layout 19 X
Xcalibur data system, errors reported by 189
V XYZ robot
Valve Check script 47 calibrating 278–286
valve position direct control 210
description 12 XYZ-axis PCB 123, 127, 129, 132
manual control 204 XYZ-axis PCB bus cable 123
Valve Tune script 50

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60053-97228 Revision B January 2013

FCC Compliance Statement

Notice on Lifting and Handling of

Notice on the Susceptibility

For manufacturing location, see the label on the instrument.

U.S. Safety and EMC (Electromagnetic Compliance) Standards

European Safety and EMC (Electromagnetic Compliance) Standards

Application of Council 2006/95/EEC “Low Voltage”: Intertek Group plc

EN61010-2-81 “Part 2-081: Particular requirements for automatic and semi-automatic

EN/(IEC) 61326-1:2006, A1(1998), A2(2001) and A3(2003) “EMC requirements for

Ole Vorm, Site Manager August 31, 2010

U.S. Safety and EMC (Electromagnetic Compliance) Standards

Canadian Safety and EMC (Electromagnetic Compliance) Standards

EN/(IEC) 61326-1:2006. Electrical equipment for measurement, control and laboratory

EN/(IEC) 61000-3-2:2006+A1+A2. Electromagnetic compatibility (EMC) - Part 3-2:

EN/(IEC) 61000-3-3:2008. Electromagnetic compatibility (EMC) - Part 3-3: Limits -

Ole Vorm, Site Manager July 19, 2011

Thermo Fisher Scientific hat Vereinbarungen mit Verwertungs-/Entsorgungsfirmen in allen EU-Mitgliedsstaaten

Electric Shock: This instrument uses

Chemical: This instrument might contain

Heat: Before servicing the instrument,

Fire: Use care when operating the system

Eye Hazard: Eye damage could occur

General Hazard: A hazard is present that

When the safety of a procedure is

Chapter 2 Maintenance Schedule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27

Thermo Scientific EASY-nLC Series Troubleshooting and Maintenance Guide xiii

Chapter 3 Maintenance Scripts and Service Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .31

Chapter 4 Routine Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .57

xiv EASY-nLC Series Troubleshooting and Maintenance Guide Thermo Scientific

Replacing a Flow Sensor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92

Chapter 5 Field Service Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .107

Chapter 6 Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .169

Thermo Scientific EASY-nLC Series Troubleshooting and Maintenance Guide xv

Troubleshooting a Pump that Fails the Flush Air Script . . . . . . . . . . . . . . . . . 212

Chapter 7 Calibrating the Autosampler’s XYZ Robot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .269

Chapter 8 Remote Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .287

Chapter 9 Returning the EASY-nLC Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .299

xvi EASY-nLC Series Troubleshooting and Maintenance Guide Thermo Scientific

Appendix A Error Codes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .303

Appendix B Mobile Phase Viscosity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .311

Appendix C Consumables and Replacement Parts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .313

Appendix D Quick Reference Guides for Routine Maintenance . . . . . . . . . . . . . . . . . . . . . . .321

Thermo Scientific EASY-nLC Series Troubleshooting and Maintenance Guide xvii

 To suggest changes to documentation or to Help

Thermo Scientific EASY-nLC Series Troubleshooting and Maintenance Guide xix

Downloading Manuals from the Customer Manuals Web Site

5. Open a list of linked PDF documents for the EASY-nLC as follows:

xx EASY-nLC Series Troubleshooting and Maintenance Guide Thermo Scientific

Safety and Special Notices

The following two stickers appear on the EASY-nLC instrument:

WARNING: SHARP NEEDLE AND MOVING PARTS.

CAUTION Highlights hazards to humans, property, or the environment. Each CAUTION

CAUTION Highlights electrical hazards to humans or property.

Thermo Scientific EASY-nLC Series Troubleshooting and Maintenance Guide xxi

CAUTION Highlights a sharp object hazard to humans.

CAUTION Highlights an eye hazard to humans.

CAUTION Highlights a chemical hazard to humans, property, or the environment.

CAUTION Highlights lifting hazards.

IMPORTANT Highlights information necessary to prevent damage to software, loss of

Note Highlights information of general interest.

Tip Highlights helpful information that can make a task easier.